Antigen-presenting cell populations and their use as reagents for enhancing or reducing immune tolerance

ABSTRACT

The present invention is based on the discovery antigen-presenting cells (APCs) may be generated to have predetermined levels of expression of the intracellular enzyme, indoleamine 2,3-dioxygenase (IDO). Because expression of high levels of IDO is correlated with a reduced ability to stimulate T cell responses and an enhanced ability to induce immunologic tolerance, APCs having high levels of IDO may be used to increase tolerance in the immune system, as for example in transplant therapy or treatment of autoimmune disorders. For example, APCs having high levels of IDO, and expressing or loaded with at least one antigen from a donor tissue may be used to increase tolerance of the recipient to the donor&#39;s tissue. Alternatively, APCs having reduced levels of IDO expression and expressing or loaded with at least one antigen from a cancer or infectious pathogen may be used as vaccines to promote T cell responses and increase immunity.

This application is a continuation of U.S. patent application Ser. No.10/121,909, filed Apr. 12, 2002.

The studies described herein were supported at least in part by Federalgrants from the National Institutes of Health (NIH R01 HL60137; NIH R01HL57930; NIH R01 A144219; NIH R21 AI49849; NIH R21 AI44759; and NIH K08HL03395), the National Institutes of Health and National CancerInstitute (NIH/NCI/RAID) and the Mason Trust Foundation. Thus, theFederal government may have rights in this invention.

FIELD OF THE INVENTION

The invention relates to the use of cell-based pharmaceuticals, and morespecifically, to the use of antigen-presenting cells (APCs) selected ascomprising immunosuppressive APCs for inducing tolerance, orimmunostimulatory APCs for inducing an increased immune response. Asexamples, immunosuppressive APCs may be used as transplant therapeutics,whereas preparations of immunostimulatory APCs may be used asanti-cancer or anti-viral vaccines.

BACKGROUND OF THE INVENTION

Once established, human tumors are not rejected by the immune system, astate of functional tolerance which eventually proves fatal to the host(Smyth, M. J., et al., Nat. Immunol. 2, 293 (2001)). Evidence frommurine models suggests that immunologic unresponsiveness may arise whentumor-associated antigens are presented by certain bone marrow-derivedtolerogenic (tolerance-producing) antigen-presenting cells (APCs)(Sotomayor, E. M., et al., Blood, 98: 1070-1077 (2001); Doan, T., etal., Cancer Res., 60: 2810-2815 (2000)). In the setting of tissuetransplantation, it would be desirable to isolate and administer suchtolerogenic APCs. However, in humans and other mammals (other thanmice), the identity of these APCs, and the mechanisms they use to inducetolerance, remain elusive.

In humans, “immature” myeloid dendritic cells (DCs) have been postulatedto function as tolerizing APCs based on findings that these cells: (1)have a decreased ability to stimulate T cell responses in vitro (Reddy,A., et al., Blood, 90: 3640-3646 (1997); Jonuleit, H., et al., Eur. J.Immunol., 27: 3135-3142 (1997)); (2) may promote the function ofimmunosuppressive or “regulatory” T cells following prolongedco-incubation (Jonuleit, H., et al., Trends Immunol., 22: 394-400(2001)); and (3) have the ability to abrogate antigen-specific T cellresponses in vivo (Dhodapkar, M. V., et al., J. Exp. Med., 193: 233-238(2001); see also U.S. Pat. Nos. 5,871,728 and 6,224,859). However, themolecular mechanism used by immature DCs or other putative tolerogenicAPCs to suppress T cell responses is unclear. Moreover, there iscurrently no way to identify or isolate tolerogenic APCs in vitro or invivo, and thus, their use as therapeutic agents is still not availablefor most applications.

More fundamentally, the supposition that immature DCs are tolerogenic isbased on an unproven and potentially flawed model of how APCs regulate Tcell activation. Thus, a prevailing model teaches that T cells arerendered unresponsive (or “tolerized”) when they receive an activationsignal (signal 1) via the T cell antigen receptor (TCR) withoutreceiving co-stimulatory signals (e.g. from CD80 and CD86) delivered onAPCs (signal 2). Immature DCs express low levels of TCR ligands (such asMHC class II antigens) and low levels of the putative costimulatorymolecules. Thus, the model teaches that immature of DCs are unable toactivate T cells because T cells receive signal 1 without adequatesignal 2.

Other findings teach against the prevailing model, and indicate thatmaturation of DCs is not necessarily associated with abrogation of Tcell suppression and/or tolerance (Albert, M. L., Nature Immunol., 2:1010 (2001); Shortman, K. et al., Nature Immunol., 2: 988-989 (2001); T.Bankenstein and T. Schuler, Trends in Immunol., 23: 171-173 (2002)).Instead, there may be a third, as yet undefined signal (signal 3) thatacts after T cells have received the signals of antigen presentation andco-stimulation (i.e. signals 1 and 2) from a fully mature APC. The thirdsignal then diverts T cells to activation or tolerance. In this model,the tolerogenic phenotype is independent of the maturation status of theAPC (in fact, maturation enhances tolerance induction) and dependsinstead on an intrinsic attribute of the APC (i.e. whether it expressessignal 3).

The inventors believe that most DC preparations are in fact mixtures ofimmunizing (stimulatory) and tolerizing APCs. The presence of a mixedpopulation of DCs in such preparations would explain why therapeuticimmunization in cancer patients using DCs remains problematic, with moststudies having only limited success (M. A. Morse and H. K. Lyerly, Curr.Opin. Mol. Ther., 2: 20 (2000)). For example, the preferred source anddifferentiation status of DCs for clinical use remains controversial(Curiel T. J., and Curiel, D. T., J. Clin. Invest., 109: 311-312, 2002).Although development of the field has been assisted by the recognitionthat the maturation state of human DCs plays an important role in theirability to stimulate effective immunity (Dhodapkar, M. V., et al., J.Clin. Invest., 105: R9-R14 (2000); Dhodapkar, M. V., et al., J. Exp.Med., 193: 233-238 (2001)), even using the best isolation and maturationstrategies and multiple tumor antigens, clinically useful therapeuticimmunization in patients with established tumors has been only partiallyeffective (Banchereau, J., et al., Cancer Res., 61: 6451-6458 (2001)).Thus, it would be useful to develop methods to isolate DCs which, ratherthan being a mixed population of activating and suppressive DCs,comprise pure activating DCs.

Conversely, these are some situations where increased tolerance toforeign antigens is desired. In one approach, immature dendritic cells(DCs) uncharacterized as suppressive or immunogenic subsets arepropagated in the presence of a cytokine regimen to maintain the cellsin an immature state. The immature cells are administered to a host inadvance of a transplant to enhance tolerance (U.S. Pat. Nos. 5,871,728and 6,224,859). However, this approach inherently sacrifices efficientantigen presentation and co-stimulation due to the immaturity of theAPCs, and risks delivering unwanted immunizing (non-tolerogenic) DCs aspart of the heterogeneous DC population. It would be helpful intransplant therapeutics to be able to create well-characterizedpopulations of mature maximally effective tolerogenic APCs which presentthe antigen subset of interest, but in a tolerizing(tolerance-promoting) preparation.

What is needed is a way to separate tolerance-inducing APCs from other(non-tolerance-inducing) APCs. The tolerance-inducing APCs can then beused in transplant procedures to promote tolerance to specific donorantigens. The non-tolerance-inducing APCs can be used in conjunctionwith undesirable foreign antigens (such as tumor antigens) as a vaccine,to prime the recipient immune system against the antigen in question.

SUMMARY OF THE INVENTION

The present invention relies on the discovery that tolerance-inducing(suppressive) antigen-presenting cells (APCs) exhibit high levels ofexpression of the intracellular enzyme indoleamine-2,3-dioxygenase(IDO), and non-tolerance-inducing (non-suppressive or T-cell activating)APCs exhibit low levels of IDO expression. IDO is both a marker for thesuppressive subset, and also the causal mechanism of suppression. Thus,the present invention describes the generation of enriched populationsof tolerance-inducing APCs and their use as therapeutics, and thegeneration of enriched populations of non-suppressive APCs and their useas therapeutics. For example, APCs having high levels of IDO (IDO⁺), andexposed to antigens from a donor may be used to increase tolerance of atransplant recipient to the donor's tissue by presenting the donor'santigens on tolerance-inducing APCs. Conversely, APCs having low levelsof IDO (IDO^(LO)) may be used to enhance responses to neo-antigens fromtumors and infectious agents.

Thus, in one aspect, the present invention comprises a method of makingantigen-presenting cells (APCs) for enhancing T cell tolerancecomprising the steps of:

(a) isolating antigen-presenting cells (APCs) or their precursors (APCprogenitors) from a first subject; and

(b) treating the cells to select for tolerance-inducing APCs expressinglevels of indoleamine 2,3-dioxygenase (IDO) enzyme activity sufficientto suppress proliferation of T cells (IDO⁺ APCs).

In another aspect, the present invention comprises a method forincreasing the number of tolerance-inducing antigen-presenting cells(APCs) in a subject comprising treating the subject to increase theproduction of antigen-presenting cells (APCs) or their precursors (APCprogenitors) expressing levels of indoleamine 2,3-dioxygenase (IDO)enzyme activity sufficient to suppress proliferation of T cells (IDO⁺APCs).

In another aspect, the present invention comprises a method forenhancing tolerance in a subject comprising the steps of:

(a) isolating antigen-presenting cells (APCs) or their precursors (APCprogenitors) from a first subject;

(b) treating the cells to select for tolerance-inducing APCs expressinglevels of indoleamine 2,3-dioxygenase (IDO) enzyme activity sufficientto suppress proliferation of T cells (IDO⁺ APCs); and

(c) administering the treated cells of step (b) to the original subjector to a second subject in an amount effective to generate atolerance-promoting immune response in the recipient subject.

The present invention also provides compositions for enhancing T celltolerance comprising APCs that express high levels of indoleamine2,3-dioxygenase (IDO) enzyme activity (IDO⁺ APCs). Such tolerizing APCsmay be used to promote acceptance of graft or transplant tissue from adonor subject in a recipient. IDO⁺ APCs may be made by the methodsdescribed herein, or by other methods in the art. Thus, in one aspect,the present invention comprises isolated antigen-presenting cells (APCs)selected as comprising APCs expressing levels of indoleamine2,3-dioxygenase (IDO) enzyme activity sufficient to suppressproliferation of T cells (IDO⁺ APCs). In another aspect, the presentinvention comprises an isolated antigen-presenting cell selected ascomprising expression of indoleamine 2,3-dioxygenase (IDO) enzymeactivity at a level sufficient to suppress proliferation of T cells. Inyet another aspect, the present invention comprises antigen-presentingcells comprising expression of indoleamine 2,3-dioxygenase (IDO) enzymeactivity at a level sufficient to suppress proliferation of T cells(IDO⁺ APCs) made by the methods of the present invention.

Alternatively, the present invention describes the generation ofimmunostimulatory (non-tolerance-inducing) APCs having reduced IDOexpression (IDO^(LO) APCs). APCs having reduced levels of IDO expressionand exposed to antigens expressed by a tumor or pathogen (such as HIV)may be used as vaccines, by presenting cancer or pathogen antigens onAPCs which contain fewer tolerance-inducing APCs.

Thus, in this aspect, the present invention comprises a method of makingantigen-presenting cells (APCs) for enhancing T cell dependentimmunologic activation in a subject comprising the steps of:

(a) isolating antigen-presenting cells (APCs) or their precursors (APCprogenitors) from a subject; and

(b) treating the isolated cells to select for APCs expressing levels ofindoleamine 2,3-dioxygenase (IDO) enzyme activity not sufficient tocause suppression of T cell proliferation (IDO^(LO) APCs).

In another aspect, the present invention comprises a method forincreasing the number of non-suppressive antigen-presenting cells (APCs)in a subject comprising treating said subject to increase the populationof antigen-presenting cells (APCs) or their precursors (APC progenitors)expressing levels of indoleamine 2,3-dioxygenase (IDO) enzyme activitynot sufficient to cause suppression of T cell proliferation (IDO^(LO)APCs).

In another aspect, the present invention comprises a method forincreasing the protective immune response in a subject comprising thesteps of:

(a) isolating antigen-presenting cells (APCs) or their precursors (APCprogenitors) from a first subject;

(b) treating the isolated cells to select for APCs expressing levels ofindoleamine 2,3-dioxygenase (IDO) enzyme activity not sufficient tocause suppression of T cell proliferation (IDO^(LO) APCs); and

(c) administering the treated cells from step (b) to the subject in anamount effective to generate a protective immune response in thesubject.

The present invention also provides compositions for increasing T cellactivation. Such compositions may be used to increase the T cellresponse to antigens in a subject. In this aspect, the present inventioncomprises isolated antigen-presenting cells (APCs) selected ascomprising APCs expressing levels of indoleamine 2,3-dioxygenase (IDO)enzyme activity not sufficient to cause suppression of T cellproliferation (IDO^(LO) APCs). In another aspect, the present inventioncomprises an isolated antigen-presenting cell (APC) selected ascomprising levels of indoleamine 2,3-dioxygenase (IDO) enzyme activitynot sufficient to cause suppression of T cell proliferation. In yetanother aspect, the present invention comprises antigen-presenting cells(APCs) comprising levels of indoleamine 2,3-dioxygenase (IDO) enzymeactivity not sufficient to cause suppression of T cell proliferation(IDO^(LO) APCs) made by the methods of the present invention.

The present invention also describes methods to quantitate the levels ofimmunosuppressive APCs in a population of APCs. Thus, in one aspcect,the present invention comprises a method to determine the number oftolerance-inducing antigen-presenting cells (APCs) in a cell populationcomprising measuring the number of cells expressing levels ofindoleamine 2,3-dioxygenase (IDO) enzyme sufficient to suppressproliferation of T cells (IDO⁺ APCs) in the population. In anotheraspect, the present invention comprises a kit for determining the numberof tolerance-inducing antigen-presenting cells (APCs) in a cellpopulation comprising reagents to measure levels of indoleamine2,3-dioxygenase (IDO) enzyme in the population of APCs, wherein thereagents are packaged in at least one individual container.

The immunosuppressive APCs may also be quantified using a biologicalassay. Thus, in another aspect, the present invention comprises a methodto quantify the ability of a population of cells to suppress T cellproliferation comprising measuring the increase in T cell proliferationin the presence of an IDO inhibitor as compared to in the absence of anIDO inhibitor. The present invention also comprises a kit fordetermining the ability of a population of antigen-presenting cells tosuppress T cell proliferation comprising an IDO inhibitor packaged in atleast one individual container.

Additionally, the present invention provides for a diagnostic assay,based on detection of IDO⁺ APCs and/or mip-3-a expression in tumors andtumor-draining lymph nodes. In this aspect, the present inventioncomprises a method for assessing the relative risk of tumor progressionin a subject comprising the steps of:

(a) assaying a sample of tissue from a tumor or tumor draining lymphnode from a subject for expression of the enzyme indoleamine2,3-dioxygenase (IDO); and

(b) correlating the risk of tumor progression to IDO expression in thetissue sample, wherein IDO expression is positively correlated with anincrease in the risk of tumor progression.

The present invention also comprises a method for assessing the risk oftumor progression in a subject comprising the steps of:

(a) assaying a sample of tissue from a tumor or tumor draining lymphnodes from a subject for mip-3α expression; and

(b) correlating the risk of tumor progression to mip-3α expression inthe tissue sample, wherein mip-3α expression is positively correlatedwith an increase in the risk of tumor progression.

The present invention also comprises kits for assessing the relativerisk of tumor progression in a subject. For example, in one aspect, thepresent invention comprises a kit for assessing the relative risk oftumor progression in a subject comprising reagents for detection of theenzyme indoleamine 2,3-dioxygenase (IDO) in a sample of tissue from atumor or tumor draining lymph node from a subject, wherein the reagentsare packaged in at least one individual container. In another aspect,the present invention comprises a kit for assessing the relative risk oftumor progression in a subject comprising reagents for detection ofrelative levels of expression of mip-3α in a sample of tissue from atumor or tumor draining lymph node from a subject, wherein the reagentsare packaged in at least one individual container.

The foregoing focuses on the more important features of the invention inorder that the detailed description which follows may be betterunderstood and in order that the present contribution to the art may bebetter appreciated. There are, of course, additional features of theinvention which will be described hereinafter and which will form thesubject matter of the claims appended hereto. It is to be understoodthat the invention is not limited in its application to the specificdetails as set forth in the following description and figures. Theinvention is capable of other embodiments and of being practiced orcarried out in various ways.

From the foregoing summary, it is apparent that an object of the presentinvention is to provide methods and compositions for enriching andisolating IDO⁺ antigen-presenting cells for use in therapeuticapplications such as the prevention of transplant rejection. Inaddition, it is apparent that an object of the present invention is toprovide methods and compositions for isolating antigen-presenting cellsdepleted of IDO⁺ antigen-presenting cells (i.e. IDO^(LO) APCs)comprising reduced suppression or tolerance, as for example in cancerprevention and therapy. These, together with other objects of thepresent invention, along with various features of novelty whichcharacterize the invention, are pointed out with particularity in theclaims and description provided herein.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows a schematic representation of a 3-step model for theregulation of IDO during dendritic cell (DC) differentiation inaccordance with an embodiment of the present invention.

FIG. 2 shows a schematic representation of methods to generate subsetsof peripheral blood-derived APCs which are either: (1) enriched intolerance-inducing APCs, as for example, for use in transplant therapy;or (2) depleted of tolerance-inducing APCs, as for example, for use inanti-cancer vaccines, in accordance with an embodiment of the presentinvention.

FIG. 3 shows a schematic representation of tolerance-inducingantigen-presenting cells (APCs) comprising expression of intracellularindoleamine 2,3-dioxygenase (IDO), cell surface markers CD123, CD11c,and the chemokine receptor CCR6 juxtaposed next to tumor cells thatexpress mip-3α, in accordance with an embodiment of the presentinvention.

FIG. 4 shows the regulation of IDO during maturation in accordance withan embodiment of the present invention wherein (A) shows DCs cultured inGMCSF+IL4 for 7 days with and without the addition of1-methyl-(D)-tryptophan; (B) shows the same DCs matured with a cocktailof cytokines (IL1β, TNFα, IL6, prostaglandin E2 (PGE2)); and (C) showsthe same DCs matured with monocyte-conditioned medium. In all groupsthere is significant IDO-mediated suppression.

FIG. 5 shows expression of CD123, the chemokine receptor CCR6, andindoleamine 2,3-dioxygenase (IDO) by antigen-presenting cells inaccordance with an embodiment of the present invention. In panels (A)and (B), human monocytes were cultured to produce myeloid dendriticcells (A) or macrophages (B), and then both groups received interferon-γduring the final 18 hrs of culture and harvested cells weretriple-stained for CD123, CD11c and IDO. In (A) and (B), panels on theright show expression of IDO and CD123 in the gated CD11c⁺ populationshown on the left. In (C) myeloid dendritic cells, cultured as in panel(A), were triple-stained for CD123, IDO, and the chemokine receptorCCR6. Both panels show the entire (ungated) population. In (D), theadherent (non-dendritic) population of APCs is shown, taken from aculture similar to panel (A) but using serum-free conditions. Cells werestained for IDO and CD123. Panel (E) compares IDO-mediated suppressionby DCs and non-dendritic APCs from the same culture where IDO-mediatedsuppression is the difference in thymidine incorporation in T cells inthe absence (stippled bars) vs. the presence (striped bars) of1-methyl-(D,L)-tryptophan (1-MT).

FIG. 6 shows suppression of allogeneic T cell proliferation byindoleamine 2,3-dioxygenase/CD123 expressing (IDO⁺/CD123⁺) dendriticcells in accordance with an embodiment of the present invention. Panel(A) shows myeloid dendritic cells which were activated for 24 hrs withTNFα, and labeled with anti-CD123 antibody and enriched by sorting(CD123⁺) with goat anti-mouse secondary antibody conjugated to magneticbeads (immunosorting), wherein the left panel shows the population priorto enrichment and the right panel shows the population after enrichment.Panel (B) shows a comparison of the effect of CD 123⁺ enriched and CD123⁺ depleted cells on allogeneic T cell proliferation as measured in amixed-leukocyte reaction by thymidine incorporation in the absence (▪)or the presence (□) of 1-methyl-(D,L)-tryptophan (1-MT; an inhibitor ofIDO). Panel (C) shows experiments similar to panel (B), using 3different pairs of donors, each allogeneic to the other, and each pairpre-tested to produce an active allogenic mixed leukocyte reaction (MLR)using sorted CD123⁺ cells without (▪) or with (□) 1-MT.

FIG. 7 shows that sorting to generate a population of cells enriched forCD123 expression (CD123⁺) by immunosorting results in APCs are enrichedfor cells having high levels of IDO expression (IDO⁺ APCs) in accordancewith an embodiment of the present invention.

FIG. 8 shows detection of IDO-expressing (IDO⁺) CD123⁺ dendritic cellsin human tumors and draining lymph nodes in accordance with anembodiment of the present invention. Panel (A) shows a positive controlfor IDO (brown) in syncytiotrophoblast cells of term human placenta(inset: the same tissue, but with anti-IDO antibody neutralized by anexcess of the immunizing peptide and shown at half scale). Panel (B)shows a malignant melanoma primary cutaneous tumor stained for IDO(arrows) (Fast Red chromogen). Panel (C) shows a draining lymph node ofa malignant melanoma, showing accumulation of IDO-expressing cells (red)in the lymphoid and perivascular regions of the node, but sparing themacrophage-rich sinuses (asterisk). Panel (D) shows a highermagnification of panel (C), with a characteristic collection ofIDO-expressing cells (dark signal) around a high-endothelial venule (V).Panel (E) shows a low-power view of a draining lymph node containingheavily pigmented metastatic melanoma cells (endogenous melanin, black;darkest signal), with confluent infiltration of IDO-expressing cell(red; next darkest signal) around the tumor deposits. Panel (F) showsnormal lymphoid tissue with scattered IDO⁺ cells (red; scattered darksignals) in a germinal center (GC) and T cell regions (T) of a humanpharyngeal tonsil from a routine tonsillectomy. Panels (G) and (H)(higher magnification of the region in panel (G) indicated by the arrow)shows co-localization of cells expressing IDO (brown; darkestcytoplasmic signal) and mip-3α (red; next darkest cytoplasmic signal) inthe lamina propria of the small intestine, particularly in thesubepithelial areas overlying mucosal lymphoid aggregates (LA). Panels(I) and (J) (higher magnification of the region in panel (I) indicatedby the arrow) shows expression of mip-3α (red) by tumor cells in alesion of malignant melanoma metastatic to lymph node, such that themip-3α⁺ cells are scattered throughout the tumor (arrow) (T), while theIDO⁺ (brown) cells are congregated at the margins of the metastasis butconfined to the residual lymph node tissue (LN).

FIG. 9 shows expression of mip-3α mRNA by human tumors in accordancewith an embodiment of the present invention. RNA from melanomas (M,n=18), renal cell carcinomas (R, n=19) or non-small cell lung cancers(L, n=9) was analyzed for expression of mip-3α by quantitative PCRcalculated as the ratio of mip-3α to the GAPDH housekeeping gene in eachsample.

DETAILED DESCRIPTION OF THE INVENTION

The present invention describes the isolation of myeloid-derivedantigen-presenting cells (APCs) which are enriched fortolerance-inducing APCs, or depleted of tolerance-inducing APCs, and theuse of these cells for various therapeutic applications. The presentinvention relies on the discovery that antigen-presenting cells may beseparated into a tolerance-inducing population, which is associated withhigh levels of expression of the enzyme indoleamine-2,3-dioxygenase(IDO), and a T cell activating (non-tolerance-inducing) population,which is associated with low levels of expression of IDO. For example,APCs having high levels of IDO (IDO⁺ APCs), and constitutivelyexpressing or exposed to donor tissue antigens may be used to increasetolerance of the recipient to the donor's tissue in transplant therapyby presenting the antigens on tolerance-inducing APCs. Alternatively,APCs having reduced levels of IDO expression (IDO^(LO) APCS) and exposedto antigens expressed by cancer tissue or virus may be used asanti-cancer vaccines or anti-viral vaccines, respectively, by presentingthe antigens on APCs depleted on tolerance-inducing cells.

Thus, the current invention teaches that conventional preparations ofhuman APCs can contain two independent subsets: an IDO⁺ subset(comprising relatively high levels of IDO expression); and an IDO^(LO)subset (comprising little to no IDO expression). Moreover, which ofthese two types of APC predominates is highly (and in some casesunpredictably) dependent on the culture conditions or other variables.In many applications, even a minor contaminating admixture of theundesired type of APC (i.e. IDO^(LO) vs. IDO⁺) may render the APCpopulation unusable, or even harmful, for the desired application. Forexample, if the goal is to generate tolerance toward donorhistocompatability antigens prior to organ transplantation, exposure toeven a minority of activating dendritic cells could promote worsenedrejection. Conversely, if the goal is to enhance responses to weak tumorantigens, the presence of even a minor population of IDO⁺tolerance-inducing cells may be enough to suppress the desired response(see e.g., Grohmann, U., et al., J. Immunol. 167: 708-714 (2001), forstudies in murine model).

Thus, in one aspect, the present invention describes a method of makingantigen-presenting cells (APCs) for enhancing T cell tolerancecomprising the steps of:

(a) isolating antigen-presenting cells (APCs) or their precursors (APCprogenitors) from a first subject; and

(b) treating the isolated cells to select for tolerance-inducing APCsexpressing levels of indoleamine 2,3-dioxygenase (IDO) enzyme activitysufficient to suppress proliferation of T cells (IDO⁺ APCs).

Preferably, the tolerance-inducing IDO⁺ APCs comprise at least 90% ofthe APC population expressing IDO at levels of at least 2-fold overbackground. More preferably, the tolerance-inducing IDO⁺ APCs compriseat least 95% of the APC population expressing IDO at levels of at least2-fold over background.

Alternatively, IDO⁺ APCs may be quantitated by measuring the biologicalactivity of the preparation. Thus, in an embodiment, thetolerance-inducing IDO⁺ APCs comprise suppressor activity, comprising anat least a 2-fold increase in T cell proliferation in the presence of anIDO inhibitor as compared to in the absence of an IDO inhibitor.Suppressor activity may be measured using a mixed leukocyte reaction orsimilar assay of T cell proliferation. Preferably, the IDO inhibitorscomprise 1-methyl-(D,L)-tryptophan, β-(3-benzofuranyl)-(D,L)-alanine,β-(3-benzo(b)thienyl)-(D,L)-alanine, or 6-nitro-(D,L)-tryptophan. Morepreferably, the IDO inhibitors comprise 1-methyl-(D)-tryptophan or6-nitro-(D)-tryptophan.

In an embodiment, the isolated APCs or APC progenitors comprise matureblood-derived dendritic cells, mature tissue dendritic cells,monocyte-derived macrophages, non-dendritic APCs, B cells, plasma cells,or any mixture thereof. Preferably, the isolated APCs or APC progenitorscomprise a cell type bearing markers of antigen presentation andcostimulatory function. Also preferably, the APCs or APC progenitors areisolated from peripheral blood, bone marrow, lymph nodes or a solidorgan from a human or other mammal.

The treatment to select for IDO⁺ APCs may comprise predetermined cultureconditions or physical selection. Preferably, step (b) comprisesculturing the cells in medium which is essentially free of serum. Alsopreferably, step (b) comprises culturing the cells in the presence ofgranulocyte-macrophage colony stimulating factor (GMCSF). Step (b) mayalso comprise culturing the cells in the presence of macrophage colonystimulating factor (MCSF). In addition, step (b) may comprise culturingthe cells in the presence of IL4. Step (b) may also comprise culturingthe cells in the presence of TGFβ and/or IL10. For example, in anembodiment, a cytokine cocktail such as those known in the art(Jonuleit, H., et al., Eur. J. Immunol., 27: 3135-3142 (1997)) may beemployed.

In an embodiment, step (b) also comprises culturing the cells with anagent to cause or regulate maturation of those APCs that express highlevels of IDO. Such maturation agents may include, but are not limitedto TNFα, IL10, TGFβ, CD40-ligand, activating anti-CD40 antibodies, cellsengineered to express cell-surface CD40-ligand, proinflammatorybacterial or pathogen products, or any combination thereof. Thus, forselection of IDO⁺ APCs these agents may be combined singly, or addedtogether with other agents used for the maturation of DCs (Jonuleit, H.,et al., Eur. J. Immunol. 27: 315-3142 (1997); Reddy, A., et al., Blood90: 3640-3646 (1997).

In an embodiment, step (b) may comprise genetically modifying the APCsor APC progenitors such that the final preparation comprises APCsexpressing levels of indoleamine 2,3-dioxygenase (IDO) enzyme activitysufficient to suppress proliferation of T cells (IDO⁺ APCs). As anexample, transfection of the culture of APCs or APC progenitors with agene for a cytokine or ligand may be employed (Kikuchi, T., et al.,Blood 98: 91-99 (2000); Gorckynski, R., et al., TransplantationProceedings 33: 1565-1566 (2001); Morita, Y., et al., J. Clin. Invest.,107: 1275-1284 (2001)).

In an embodiment, the method utilizes cell surface proteins or othermarkers for separation (enrichment or depletion) of IDO⁺ cells fromother APCs. Thus, in an embodiment, the method includes measuringexpression of at least one cell surface marker that identifies the APCsas expressing levels of IDO sufficient to suppress T cell proliferation(IDO⁺ APCs) or as expressing levels of IDO not sufficient to suppress Tcell proliferation (IDO^(LO) APCs). Preferably, the cell surface markeris used to separate IDO⁺ APCs from IDO^(LO) APCs. The markers used fordifferential selection of IDO⁺ cells from IDO^(LO) cells include, butare not limited to, CD123, CD11c, CCR6, CD14 or any combination thereof.Alternatively, the method may include differential adhesion to asubstrate to separate APCs that expressing levels of IDO sufficient tosuppress T cell proliferation (IDO⁺APCs) from APCs expressing levels ofIDO not sufficient to suppress T cell proliferation (IDO^(LO) APCs).

One object of the present invention is to develop tolerance-promotingAPCs that present a specific subset of antigens of interest. Forexample, tolerance-promoting ACPs that present antigens from a donor maybe administered to a transplant recipient to promote acceptance of agraft or transplant. Thus, in an embodiment, the subject from which theAPCs or APC progenitors are isolated comprises a tissue donor to asecond subject. In another embodiment, the APCs or APC progenitors areisolated from a subject with an autoimmune disorder for subsequentpreparation of IDO⁺ APCs for use in treating the disorder.

In addition, the treated APCs may be exposed to at least one source ofantigen after isolation from a subject and treatment to select for IDO⁺APCs. In an embodiment, the antigen comprises a purified, or a syntheticor recombinant polypeptide representing a specific antigen to which itis desired that tolerance be induced, or a short synthetic polypeptidefragment derived from the amino acid sequence of such an antigen.Preferably, the source of antigen comprises antigens expressed by adonor tissue graft. Also preferably, the source of antigen comprisesprotein or other material to which a patient has an autoimmune disorder(see e.g. Yoon, J.-W., et al., Science 284: 1183-1187 (1999) forexamples of such proteins). In yet another embodiment, the methodcomprises transfecting or genetically engineering the IDO⁺ APCs toexpress at least one antigenic polypeptide.

The tolerance-inducing APCs or their precursors (or non-toleranceinducing APCs or their precursors) as defined by the methods of thepresent invention may also be increased in number in a subject byadministering to the subject agents that increase the number of thedesired APCs. Numerous cytokines and other agents have been shown toincrease the number of one or more of different types of APCs whenadministered in vivo. Examples of such agents include MCSF, GMCSF,granulocyte colony-stimulating factor (GCSF), FLT3-ligand, and othernatural and artificial cytokines and hematopoietic growth factors.Previously, however, it was not known whether the APCs induced by suchtreatments were tolerance-inducing or non-tolerance-inducing or amixture of both. The present invention provides the discovery that bymeasuring IDO expression following isolation and in vitro treatment ofthe desired APC population, the effectiveness of such in vivo treatmentscan be evaluated and improved upon. In addition, as described herein,the present invention provides methods to quantify IDO expression, bothon a cell-by-cell basis and as a biologicial assay for bulk populations.Thus, in an embodiment, tolerogenic APCs or their precursors inperipheral blood from a donor may be increased by treatment withselected cytokines prior to isolation for in vitro culture and deliveryto a recipient for the purpose of inducing transplantation tolerance.

Thus, in one aspect, the present invention comprises a method forincreasing the number of tolerance-inducing antigen-presenting cells(APCs) in a subject comprising treating the subject to increase theproduction of APCs or their precursors (APC progenitors) expressinglevels of indoleamine 2,3-dioxygenase (IDO) enzyme activity sufficientto suppress proliferation of T cells (IDO⁺ APCs).

In another aspect, the present invention comprises a method forenhancing tolerance in a subject comprising the steps of:

(a) isolating antigen-presenting cells (APCs) or their precursors (APCprogenitors) from a first subject;

(b) treating the cells to select for APCs expressing levels ofindoleamine 2,3-dioxygenase (IDO) enzyme activity sufficient to suppressproliferation of T cells (IDO⁺ APCs); and

(c) administering the treated cells of step (b) to the original subjector to a second subject in an amount effective to generate atolerance-promoting response in said recipient subject.

Preferably, the tolerance-promoting response reduces T cell activationin the recipient subject. Also preferably, the tolerance-promotingresponse prolongs the survival of transplanted cells or tissues in therecipient subject. Also preferably, the tolerance-promoting responsereduces the symptoms of an autoimmune disease in the recipient subject.

In an embodiment, the subject from which the APCs or APC progenitors areisolated comprises a tissue donor to the recipient subject. In anotherembodiment, the subject from which the APCs or APC progenitors areisolated comprises a mammal with an autoimmune disorder.

The method may include exposing the APCs or APC progenitors to at leastone source of antigen after isolation from the first subject andtreatment to select for IDO⁺ APCs. Preferably, the antigen comprises asynthetic or natural polypeptide. Also preferably, the antigen comprisesat least one antigen expressed by a donor tissue graft. Alternatively,the antigen may comprise at least one antigen to which the recipientsubject has an autoimmune disorder. In another embodiment, the methodmay comprise transfecting or genetically engineering the APCs selectedas IDO⁺ to express at least one antigenic polypeptide.

The present invention also provides compositions for enhancing T celltolerance. Such tolerizing APCs may be used to promote acceptance ofgraft or transplant tissue from a donor subject in a recipient or totreat a patient with autoimmune disease. In this aspect, the presentinvention comprises isolated antigen-presenting cells (APCs) selected ascomprising APCs expressing levels of indoleamine 2,3-dioxygenase (IDO)enzyme activity sufficient to suppress proliferation of T cells (IDO⁺APCs). In another aspect, the present invention comprises an isolatedantigen-presenting cell selected as comprising expression of indoleamine2,3-dioxygenase (IDO) enzyme activity at a level sufficient to suppressproliferation of T cells. In yet another aspect, the present inventioncomprises antigen-presenting cells comprising expression of indoleamine2,3-dioxygenase (IDO) enzyme activity at a level sufficient to suppressproliferation of T cells (IDO⁺ APCs) made by the methods of theinvention.

Preferably, the isolated IDO⁺ APCs comprise at least 90% of the APCpopulation expressing IDO at levels of at least 2-fold over background.More preferably, the isolated IDO⁺ APCs comprise at least 95% of the APCpopulation expressing IDO at levels of at least 2-fold over background.Also preferably, the isolated IDO⁺ APCs comprise suppressor activitycomprising an at least a 2-fold increase in T cell proliferation in thepresence of an IDO inhibitor as compared to in the absence of an IDOinhibitor. In an embodiment, the isolated IDO⁺ APCs express at least oneantigenic polypeptide.

In an embodiment, the isolated cells comprise at least one cell surfacemarker that identifies the cells as expressing levels of indoleamine2,3-dioxygenase (IDO) enzyme activity sufficient to suppress T cellproliferation (IDO⁺ APCs). Preferably, the marker comprises CD123, CD11cand CCR6.

In an embodiment, the composition of the present invention includes apharmaceutically acceptable carrier. Also preferably, the composition ofthe present invention includes one or more immunosuppressivepharmaceuticals in a unit dosage form.

In another aspect, the present invention comprises the generation ofimmunostimulatory cells. Such cells may be used to stimulate the immuneresponse, as for example, to cancer-related antigens or viral-relatedantigens. Thus, in this aspect, the present invention comprises a methodof making antigen-presenting cells (APCs) for enhancing T cell dependentimmunologic activation in a subject comprising the steps of:

(a) isolating antigen-presenting cells (APCs) or their precursors (APCprogenitors) from a subject; and

(b) treating the isolated cells to select for APCs expressing levels ofindoleamine 2,3-dioxygenase (IDO) enzyme activity not sufficient tocause suppression of T cell proliferation (IDO^(LO) APCs).

Preferably, the IDO^(LO) APCs comprise a population of APCs having lessthan 10% of the population expressing IDO at a level of greater than2-fold over background. More preferably, the IDO^(LO) APCs comprise apopulation of APCs having less than 5% of the population expressing IDOat a level of greater than 2-fold over background.

Alternatively, the IDO^(LO) APCs may be quantitated using a T cellproliferation assay such as a mixed leukocyte reaction or similarmethods, wherein IDO^(LO) APCs comprise an absence of suppressoractivity comprising a less than a 1.5-fold increase in T cellproliferation in the presence of an IDO inhibitor as compared to in theabsence of an IDO inhibitor. Preferably, the IDO inhibitor comprises1-methyl-(D,L)-tryptophan, β-(3-benzofuranyl)-(D,L)-alanine,β-(3-benzo(b)thienyl)-(D,L)-alanine, or 6-nitro-(D,L)-tryptophan. Alsopreferably, the IDO inhibitor comprises 1-methyl-(D)-tryptophan or6-nitro-(D)-tryptophan.

Preferably, the isolated APCs or APC progenitors comprise matureblood-derived dendritic cells, mature tissue dendritic cells,monocyte-derived macrophages, non-dendritic APCs, B cells, plasma cells,or any mixture thereof. Also preferably, the isolated APCs or APCprogenitors comprise a cell type bearing markers of antigen presentationand costimulatory function. Also preferably, the APCs or APC progenitorsare isolated from peripheral blood, bone marrow, lymph nodes or a solidorgan from a human or other mammal.

The treatment to select for IDO^(LO) APCs may comprise predeterminedculture conditions or physical selection. In an embodiment, treatment ofAPCs and progenitor APCs to select for IDO^(LO) APCs comprises culturingthe cells in the presence of serum-free medium. In other embodiments,treatment of APCs and progenitor APCs to select for IDO^(LO) APCscomprises culturing the cells in the presence of MCSF, or GMCSF, orinterferon-α, or combinations thereof. In an embodiment, treatment ofAPCs and progenitor APCs to select for IDO^(LO) APCs comprises culturingthe cells with an agent to cause maturation of those APCs that expresslow levels of IDO (IDO^(LO) APCs). Preferably, the maturation agentscomprise TNFα, CD40-ligand (CD40L), activating anti-CD40 antibodies,cells engineered to express cell-surface CD40-ligand, proinflammatorybacterial or pathogen products, or any combination thereof.Alternatively (or additionally), the APCs may genetically engineered toexpress CD40-ligand. The treatment may also comprise culturing the cellsin the presence of neutralizing antibodies for IL10 and/or TGFβ. Thus,for selection of IDO^(LO) APCs, these agents may be combined singly, oradded together with other agents used for the maturation of DCs(Jonuleit, H., et al., Eur. J. Immunol. 27: 315-3142 (1997); Reddy, A.,et al., Blood 90: 3640-3646 (1997).

Alternatively, step (b) may comprise genetically modifying the APCs orAPC progenitors such that the final preparation comprises APCsexpressing levels of indoleamine 2,3-dioxygenase (IDO) enzyme activitynot sufficient to suppress T cell proliferation (IDO^(LO) APCs).

In an embodiment, the method utilizes cell surface proteins or othermarkers for selection of IDO^(LO) cells from other APCs. Thus, in anembodiment, the method includes measuring expression of at least onecell surface marker that identifies the APCs as expressing levels of IDOnot sufficient to suppress T cell proliferation (IDO^(LO)) or asexpressing levels of IDO (IDO⁺). Preferably, the cell surface marker isused to separate APCs that express low levels of IDO (IDO^(LO) APCs)from APCs that express high levels of IDO sufficient to suppress T cellproliferation (IDO⁺ APCs). The markers used for differential selectionof IDO^(LO) cells from IDO⁺ cells include, but are not limited to,CD123, CD11c, CCR6, CD14 or any combination thereof. Alternatively, themethod may include differential adhesion to a substrate to separate APCsthat express levels of IDO not sufficient to suppress T cellproliferation (IDO^(LO) APCs) from APCs that express levels of IDOsufficient to suppress T cell proliferation (IDO⁺ APCs).

One object of the present invention is to develop immunogenic APCs thatpresent a specific subset of antigens of interest. For example, APCsdepleted of tolerance-inducing cells (i.e. IDO^(LO) APCs) may be used topresent antigens expressed by a tumor or a pathogen to a subject toincrease the immune response to such antigens. Thus, in an embodimentthe method includes exposing the treated APC preparation to at least onesource of antigen after isolation and selection of IDO^(LO) APCs. In anembodiment, the antigen comprises a at least one synthetic or naturalpolypeptide. Preferably, the antigen is expressed by a tumor. Alsopreferably, the antigen is expressed by a pathogen. Alternatively, themethod may comprise transfecting or genetically engineering the IDO^(LO)APCs to express at least one antigenic polypeptide.

In another aspect, the present invention comprises a method forincreasing the number of non-suppressive antigen-presenting cells (APCs)in a subject comprising treating the subject to increase the populationof APCs or their precursors (APC progenitors) expressing levels ofindoleamine 2,3-dioxygenase (IDO) enzyme activity not sufficient tocause suppression of T cell proliferation (IDO^(LO) APCs).

In another aspect, the present invention comprises a method forincreasing the protective immune response in a subject comprising thesteps of:

(a) isolating antigen-presenting cells (APCs) or their precursors (APCprogenitors) from a first subject;

(b) treating the isolated cells to select for APCs expressing levels ofindoleamine 2,3-dioxygenase (IDO) enzyme activity not sufficient tocause suppression of T cell proliferation (IDO^(LO) APCs); and

(c) administering the treated cells of step (b) back into the subject inan amount effective to generate a protective immune response in thesubject.

Preferably, a protective immune response comprises a reduction inproliferation of tumor cells or a reduction in the clinical progressionof a malignancy. Also preferably, a protective response is associatedwith a reduced pathogen load or increased resistance to at least onepathogen.

In an embodiment, the method is used to increase the immune response toa specific subset of antigens. Thus, in an embodiment, the methodincludes exposing the treated cells of step (b) to at least one sourceof antigen after isolation from the first subject. In an embodiment, theantigen comprises an natural or synthetic polypeptide. Preferably, theantigen is expressed by a tumor. Also preferably, the antigen isexpressed by a pathogen. In another embodiment, the method comprisestransfecting or genetically engineering the treated cells of step (b) toexpress at least one antigenic polypeptide.

The present invention also provides composition for increasing T cellactivation. Such compositions may be used to increase the T cellresponse to antigens in a subject. In this aspect, the present inventioncomprises isolated antigen-presenting cells (APCs) selected ascomprising APCs expressing levels of indoleamine 2,3-dioxygenase (IDO)enzyme activity not sufficient to cause suppression of T cellproliferation (IDO^(LO) APCs). In another aspect, present inventioncomprises an isolated antigen-presenting cell (APC) selected ascomprising levels of indoleamine 2,3-dioxygenase (IDO) enzyme activitynot sufficient to cause suppression of T cell proliferation. In yetanother aspect, the present invention comprises antigen-presenting cells(APC) comprising levels of indoleamine 2,3-dioxygenase (IDO) enzymeactivity not sufficient to cause suppression of T cell proliferation(IDO^(LO) APCs) made by the methods of the invention.

Preferably, the IDO^(LO) cells comprise a population of APCs having lessthan 10% of the population expressing IDO at a level of greater than2-fold over background. More preferably, the IDO^(LO) cells comprise apopulation of APCs having less than 5% of the population expressing IDOat a level of greater than 2-fold over background. Also preferably, theIDO^(LO) APCs comprise an absence of suppressor activity comprising lessthan a 1.5-fold increase in T cell proliferation in the presence of anIDO inhibitor as compared to in the absence of an IDO inhibitor.

In an embodiment, the IDO^(LO) APCs comprise at least one cell surfacemarker that identifies the cells as expressing levels of indoleamine2,3-dioxygenase (IDO) enzyme activity not sufficient to causesuppression of T cell proliferation (IDO^(LO)). Preferably, the markercomprises CD14. Also preferably, the marker causes preferential adhesionof the cells to plastic. Preferably, the composition comprises apharmaceutically acceptable carrier.

APCs as IDO⁺ and IDO^(LO) Populations

The present invention relies on the discovery that APCs expressing highlevels of the intracellular enzyme indoleamine 2,3-dioxygenase (IDO) arecapable of suppressing T cell responses in vitro and in vivo. Thus, thepresent invention is based on the discovery that thetryptophan-degrading enzyme indoleamine 2,3-dioxygenase (IDO) is anintrinsic attribute of APCs that determines whether or not the APC isimmunosuppressive or immunostimulatory.

Immunologic tolerance is operationally defined as the absence of animmunologic rejection response toward specific tissues or antigens.Conceptually, there are two types of tolerance: pre-existing toleranceto self, and acquired tolerance to new antigens. For example,imunocompetent mice become anergic (non-reactive) even to non-selfantigens when these are introduced on tumors (Staveley-O'Carroll, K., etal., Proc. Natl. Acad. Sci. USA, 95: 1178-1183 (1998)). This anergy isapparently caused, not by the tumor cells themselves, but bycross-presentation of tumor antigens by tolerogenic bone marrow-derivedAPCs (Sotomayor, E. M., et al., Blood, 98: 1070-1077 (2001)).

Tolerogenic APCs are potent regulators of the immune response becausethey can create networks of immunoregulatory (suppressor) T cells. Theseregulatory T cell networks are apparently involved in both maintainingnormal tolerance to self, and also in mediating a state of acquiredunresponsiveness to non-self antigens (e.g. Sakaguchi, S., Cell, 101:455-459 (2000); H. Waldmann and S. Cobbold, Immunity, 14: 399-406(2001); Shevach, E. M., J. Exp. Med., 193: F41-F46 (2001)). For example,it has been shown that tumor-specific regulatory T cells exist, and thatblocking or depleting these cells facilitates the ability to breaktolerance to tumor antigens (Sutmuller, R. P. M., et al., J. Exp. Med.,194: 823-832 (2001); van Elsas, A., et al., J. Exp. Med., 190: 355-366(1999); van Elsas, A., et al., J. Exp. Med., 194: 481-490 (2001)). Onceestablished, this type of unresponsiveness is self-perpetuating,transferable, and can even “spread” to encompass new antigensencountered in the same context as those to which the network is alreadytolerant (S. Cobbold and H. Waldmann, Curr. Opin. Immunol., 10: 518-524(1998)). When present, regulatory T cells tend to be dominant, enforcingfunctional tolerance throughout the entire immune system even in theface of other, non-tolerant T cells (Honey, K., et al., Immunol. Res.,20: 1-14 (1999)). It is known that certain types of human APCs are ableto promote such regulatory T cells (Jonuleit, H., Trends in Immunol. 22:394-400 (2001); Dhodapkar, M. V., et al., J. Exp. Med., 193: 233-238(2001)). However the mechanism by which this occurs is unknown. Clearly,the ability to create such potent regulatory T cells is highly desirablein settings such as organ transplantation or autoimmunity. Conversely,it is undesirable (but often occurs) to inadvertently create such cellswhen immunizing against antigens (e.g. from pathogens or tumors).

The enzyme indoleamine 2,3-dioxygenase (IDO) is an intracellularheme-containing enzyme that catalyzes the initial rate-limiting step intryptophan degradation along the kynurenine pathway (M. W. Taylor and G.Feng, FASEB J., 5, 2516-2522 (1991)). It has been proposed that IDOsuppresses T cell proliferation by degrading tryptophan in the localenvironment (Munn, D. H., et al., J. Exp. Med., 189: 1363-1372 (1999)).Two types of human APCs, (1) monocyte-derived macrophages (Munn, D. H.,et al., J. Exp. Med., 189: 1363-1372 (1999)), and (2) monocyte-deriveddendritic cells (Hwu, P., et al., J. Immunol. 164: 3596-3599 (2000)),which suppress T cell activation in vitro have been shown to express thetryptophan-degrading enzyme indoleamine 2,3-dioxygenase (IDO). In mice,IDO has been implicated in the tolerance displayed by the maternalimmune system toward the immunologically disparate fetus (Mellor, A. L.,et al., Nat. Immunol. 2: 64-68 (2001); Munn, D. H., et al., Science,281: 1191-1193 (1998)), as well as in acquired tolerance toward antigenspresented by murine CD8α⁺ dendritic cells (Grohmann, U. et al., J.Immunol., 167: 708-714 (2001)). Also, IDO is required for the inductionof spontaneous tolerance by liver allografts (Miki, T., et al.,Transplantation Proceedings 33: 129-130 (2000)), a process which isthought to be mediated by graft associated DCs (Thompson, A. W. and Lu.,L., Immunol. Today 20: 27-31 (1999)). A direct mechanistic link betweenIDO gene expression and suppression of antigen-specific T cell responsesin vivo has been shown in a mouse model by the inventors (Mellor, A. L.,et al., J. Immunol. 168: 3771-3776 (2002)), wherein transfection of themouse IDO gene into murine cell lines causes: (1) suppression of T cellresponses to antigens presented by the IDO-expressing cell lines; and(2) abrogation of the ability of the cells to prime an allogenic T cellresponse in vivo to antigens.

There are several ways to measure IDO expression. As defined herein,cells comprising high levels of IDO activity comprise: (1) a level ofIDO activity sufficient to suppress T cell proliferation either in vitroor in vivo; (2) a level of IDO protein or RNA significantly above thebackground level of the assay; or (3) at least 90% of APCs in thepreparation expressing IDO as enumerated on a cell-by-cell basis. Forexample, high level IDO expression (IDO⁺) is defined by flow cytometryquantitatively on a cell by cell basis as expression of antigenic IDOprotein at a level of at least 2-fold above background, more preferably,at a level of at least 5-fold above background, and even morepreferably, at a level of at least 10-fold over background. In thisassay, background may be defined as neutralization of an anti-IDOantibody using standard techniques such as binding with an excess of animmunizing peptide (polyclonal antibody assay) or binding of anisotype-matched control (monoclonal antibody assay). Thus, in anembodiment of the present invention, tolerance-inducing IDO⁺ APCscomprise at least 90% of the APC population expressing IDO at levels ofat least 2-fold over background, and more preferably, at least 95% ofthe APC population expressing IDO at levels of at least 2-fold overbackground.

IDO protein and RNA levels can also be measured by other techniquesincluding western blot, immunohistochemistry, northern blot,reverse-transcriptase polymerase chain reaction (RT-PCR), or in situhybridization. Preferably, using the techniques of immunohistochemistryor in situ hybridization, IDO expression is be measured on acell-by-cell basis. Cells expressing IDO are defined relative to theappropriate negative control for the particular assay as understood byone skilled in the art. Preferably, the IDO-expressing APCs comprise atleast 90% of the APC population in such an assay, and more preferably,at least 95% of the APC population. IDO can also be measured by westernblot, northern blot, RT-PCR, and other assays that measure IDO in a bulkpopulation. High level IDO expression (IDO⁺) for a bulk population isdefined as IDO-specific signal of at least 2-fold over the negativecontrol for the particular assay; as understood by one skilled in theart, or preferably, at a level of at least 5-fold over background, andmore preferably, at a level of at least 10-fold over background.

Low levels of IDO expression (IDO^(LO)) may also be defined by flowcytometry or other assays quantitatively on a cell-by-cell basis withreference to the percentage of cells expressing IDO. Thus, in anembodiment, IDO^(LO) cells comprise APCs wherein a minority of APCs inthe preparation expressing IDO protein at a level of at least 2-foldover background. In an IDO^(LO) preparation of APCs, preferably lessthan 10% of the APCs express IDO protein at a level of at least 2-foldover background, more preferably less than 5% of the APCs express IDOprotein at a level of at least 2-fold over background. Alternatively,IDO is measured by immunohistochemistry, in situ hybridization or othertechniques that measure IDO on a cell-by-cell basis, and an IDO^(LO)preparation is defined as comprising less than 20% IDO-expressing cells,or more preferably less than 10% IDO-expressing cells, and even morepreferably, less than 5% IDO-expressing cells. Alternatively, IDOexpression is measured in a bulk population, such that IDO-specificsignal is less than 2-fold over the negative control for the particularassay.

Alternatively, an assay to measure biological activity such as a T cellproliferation assay is used to quantify IDO activity. A T cellproliferation assay includes, but is not limited to, a mixed leukocytereaction (MLR) assay, or stimulation of T cells with antigen or mitogen.

Thus, in an embodiment, high level IDO expression (IDO⁺) is defined as agreater than 2-fold increase in T-cell proliferation when an inhibitorof IDO is added to MLRs containing the preparation of interest. Thisassay provides a physiological basis to quantify the amount of T-cellproliferation that has been suppressed by IDO (i.e. the MLR without theIDO inhibitor compared to the MLR with the IDO inhibitor). Preferably,the MLR contains the APC preparation to be administered plus allogeneicor xenogeneic T cells. Alternatively, the T cell proliferation assay maycontain the APC preparation to be administered plus autologous T cellsand an antigen or mitogen to serve as the stimulus for T cellproliferation. High level IDO expression (IDO⁺) is defined as a greaterthan 2-fold increase in T cell proliferation when an inhibitor of IDO isadded to co-cultures containing the preparation of interest.

T cell proliferation assays may also be used to quantify low IDOactivity. Thus, in an embodiment, low IDO activity (IDO^(LO)) is definedby an allogenic MLR or autologous antigen or mitogen-stimulation assayas less than 1.5 fold increase in T cell proliferation when an inhibitorof IDO is added to co-cultures containing the APC preparation ofinterest.

As defined herein, an inhibitor of IDO is an agent capable of preventingtryptophan degradation and/or kynurenine production by IDO enzyme in acell free system, or by cells expressing IDO. For example, the inhibitorof IDO is an agent capable of preventing tryptophan degradation and/orkynurenine production by isolated human monocyte-derived macrophagesactivated by interferon-γ (Munn, D. H., et al., J. Exp. Med., 189:1363-1372 (1999)). Preferably, the inhibitor of IDO is an analogue oftryptophan. More preferably, the inhibitor of IDO is the (D) isomeranalogue of tryptophan rather than the (L) analogue, as in some casesonly the (D) isomer reveals true suppression of T-cell activation byIDO. Thus in an embodiment, the inhibitor of IDO comprises1-methyl-(D,L)-tryptophan, β-(3-benzofuranyl)-DL-alanine (the oxygenanalog of tryptophan) (1-MT), β-[3-benzo(b)thienyl]-(D,L)-alanine (thesulfur analog of tryptophan) (S. G. Cady and M. Sono, Arch. Biochem.Biophys. 291, 326 (1991)), or 6-nitro-(D,L)-tryptophan. More preferably,the inhibitor of IDO comprises 1-methyl-(D)-tryptophan or6-nitro-(D)-tryptophan.

Thus, the present invention describes a method of makingantigen-presenting cells (APCs) for enhancing T-cell tolerancecomprising the steps of:

(a) isolating antigen-presenting cells (APCs) or their precursors (APCprogenitors) from a first subject; and

(b) treating the isolated cells to select for APCs expressing levels ofindoleamine 2,3-dioxygenase (IDO) enzyme activity sufficient to suppressproliferation of T cells (IDO⁺ APCs).

The present invention also describes a method of makingantigen-presenting cells (APCs) for enhancing T-cell activation in anindividual comprising the steps of:

(a) isolating antigen-presenting cells (APCs) or their precursors (APCprogenitors) from a subject; and

(b) treating the isolated cells to select for APCs expressing levels ofindoleamine 2,3-dioxygenase (IDO) enzyme activity not sufficient tocause suppression of T cell proliferation (IDO^(LO) APCs).

As defined herein, isolated APCs or progenitor APCs comprise populationsof cells which are either able to express high levels of IDO (IDO⁺ APCs)or which constitutively express low levels of IDO (IDO^(LO) APCs) asmeasured by protein levels (flow cytometry), mRNA levels, or T cellproliferation assays. The isolated APCs or APC progenitors may comprisemature blood-derived dendritic cells, mature tissue dendritic cells,monocyte-derived macrophages, non-dendritic APCs, B cells, plasma cells,or any mixture thereof. In an embodiment, the isolated APCs or APCprogenitors comprise a cell type bearing markers of antigen presentationand costimulatory function.

As defined herein, non-dendritic APCs comprise cells isolated directlyfrom peripheral blood, bone marrow, or solid organ or tissue, or derivedby in vitro culture of cells from peripheral blood, bone marrow, orsolid organ or tissue, which cells do not express CD83, but which doexpress high levels of MHC class II antigen as well as at least onemarker of APC function. Such markers of APC function include, but arenot limited to, CD80, CD86, and B7-H1 (Dong et al., Nature Med., 5:1365-1369 (1999)). Such non-dendritic APCs may express high constitutiveor inducible levels of IDO (IDO⁺), low levels of IDO (IDO^(LO)), or maycomprise a mixture of IDO⁺ and IDO^(LO) cells. Non-dendritic APCsinclude, but are not limited to, endothelial cells, tissue macrophages,and other cells expressing constitutive or inducible MHC II.

Non-dendritic APC include cultured blood-derived non-dendritic APCs. Asdefined herein, cultured blood-derived non-dendritic APCs compriseisolated peripheral blood mononuclear cells or a fraction thereof whichfollowing culture in vitro, do not express CD83 but do express highlevels of MHC class II antigens as well as one or more markers of APCco-stimulatory function, such as, but not limited to, CD80, CD86 orB7-H1 (Dong et al., Nature Med., 5: 1365-1369 (1999)), eitherconstitutively or following exposure to maturation agents. Blood-derivednon-dendritic APCs may be cultured in a medium with or without cytokinesincluding, but not limited to, MCSF, GMCSF, IL4, IL3, IL 10, and TNFα.For example, in an embodiment, monocyte derived macrophages cultured inMCSF express high levels of IDO (IDO⁺) (Munn, D. H., et al., J. Exp.Med., 189: 1363-1372 (1999)). In another embodiment, CD14+/CD83-cellsfollowing culture in GMCSF+IL4 (which differentially adhere to plasticculture dishes) show no IDO mediated suppression (IDO^(LO)).

As defined herein, dendritic cells (DCs) comprise cells isolateddirectly from peripheral blood, bone marrow, organs or tissues, orderived by culture of cells isolated form peripheral, bone marrow,organs, tissues, or isolated CD34⁺ stem cells collected from peripheralblood or bone marrow which cells express CD83 constitutively orfollowing culture and maturation. DCs may be cultured in medium with orwithout cytokines, including, but not limited to GMCSF, IL4, IL3, andIL10.

Thus, as defined herein, immature dendritic cells (DCs) comprise DCswhich express low levels of MHC class II antigens. As defined herein,low levels of MHC class II antigens are levels less than 2-fold greaterthan the negative control used in the assay to measure MHC class IIantigen expression. Low levels of MHC class II may also be determined bycomparison to mature DCs, and preferably comprise less than half thelevel of expression of MHC class II antigens found on mature DCs. MHCclass II antigens may be measured by flow cytometry or other methodsknown in the art.

As defined herein, mature dendritic cells (DCs) comprise DCs whichconstitutively express high levels of MHC class II, or which have beentreated with agents to cause maturation. As defined herein, high levelsof MHC class II antigens are levels at least 2-fold greater than thenegative control used in the assay to measure MHC class II antigenexpression. Maturation can also be defined by comparison with the samepopulation of DCs prior to treatment with agents to induce maturation.Defined in this way, maturation comprises at least a 2-fold upregulationof MHC class II antigen. Agents causing maturation comprise TNFα,CD40-ligand (CD40L), activating anti-CD40 antibodies, cells engineeredto express cell surface CD40-ligand, or bacterial or pathogen products.

As defined herein, B cells comprise cells isolated from blood, bonemarrow, lymph nodes or other tissue which express one or more markers ofB cell differentiation such as, but not limited to, CD19, CD20, CD21, orsurface immunoglobulin, wherein B cell markers may be measured by flowcytometry or other methods known in the art.

As defined herein, plasma cells comprise cells isolated from blood,lymph node or other tissue which express CD38 and cytoplasmicimmunoglobulin as measured by flow cytometry or other methods known inthe art.

As defined herein, selection of APCs which comprise IDO⁺ APCs orIDO^(LO) APCs may comprise selective culturing of the cells, including apredetermined regimen of cytokines and/or maturation agents. Forexample, a cytokine cocktail such as those known in the art (Jonuleit,H., et al., Eur. J. Immunol., 27: 3135-3142 (1997)) may be employed.Thus, for selection of IDO⁺ APCs or IDO^(LO) APCs, cytokines may becombined singly, or added together with other agents used for thematuration of DCs (Jonuleit, H., et al., Eur. J. Immunol. 27: 315-3142(1997); Reddy, A., et al., Blood 90: 3640-3646 (1997)). Selection alsocomprises physical selection techniques such as selecting immunosortingof either IDO⁺ or IDO^(LO) cells. This is possible in that certaincell-surface antigens are associated with the IDO⁺ and IDO^(LO)phenotypes in APCs. In another embodiment, sorting comprisesdifferential adherence of either IDO^(LO) or IDO⁺ cells to a substrate,presumably due to the expression of a specific cell surface marker thatincreases adherence.

T cell responses comprise allogeneic, xenogeneic, mitogen-driven, orantigen-driven responses. As defined herein, allogeneic T cells compriseT cells from a different individual of the same species, wherein such Tcells proliferate in response to the presence of antigenic differencesbetween the individuals. Xenogeneic T cells comprise T cells from anindividual of a different species, wherein such T cells proliferate inresponse to the presence of antigenic differences between the species.As an example, T cells from a human recipient are xenogeneic to aporcine tissue donor.

As defined herein, CD40-ligand (CD40L) comprises isolated polypeptides,multimers of such peptides, or other compositions that bind to theextracellular binding region of a CD40 receptor of human, porcine orother origin (e.g. U.S. Pat. No. 6,290,972, incorporated by reference inits entirety herein).

As defined herein, proinflammatory bacterial and pathogen productscomprise materials isolated from bacteria or other pathogens, orsynthetic compositions derived from compounds produced by suchorganisms, including, but not limited to, lipopolysaccharide, CpG DNA,or monophosphoryl lipid A, which have as their defining property thatthey cause up-regulation of MHC class II molecules and/or costimulatorymolecules (CD80 or CD86) on immature dendritic cells or non-dendriticAPCs.

Thus, the present invention relies on the discovery that APCs mayexpress high levels of IDO (IDO^(+/POS)) or low levels of IDO(IDO^(LO/NEG)) depending upon their hematopoietic lineage or state ofmaturation including the effect of conditioning and/or licensing signalsencountered during development. As an example, FIG. 1 summarizes aproposed 3-step model for the regulation of IDO in the specific case ofmonocyte-derived dendritic cell DC differentiation. In step 1, monocytesbegin to differentiate along the DC lineage. Step 2 occurs during laterDC differentiation and maturation, when there is a cryptic commitment ofeach individual DC to subsequently become either IDO^(+/POS) orIDO^(LO/NEG). In an embodiment, those DCs that are negative for the cellsurface marker CD123 commit to becoming IDO-negative (IDO^(LO/NEG)),suggesting that there is some degree of inherent heterogeneity or“pre-commitment” within in the circulating monocyte pool. In contrast,cells that are CD123 positive (CD123⁺) still have the option to becomeeither functionally IDO^(+/POS) or IDO^(LO/NEG), based on the conditionspresent during maturation. Thus, the CD123⁺ cells will commit to theIDO^(LO/NEG) (non-suppressor) phenotype if step 2 is driven solely bypro-inflammatory factors (e.g., CD40L, TNFα). If counter-regulatorycytokines such IL10 or TGFβ are present during maturation, then theCD123⁺ cells will commit to the IDO^(+/POS) (suppressor) phenotype.

Although the cells are committed at step 2, the functional IDO^(+/POS)phenotype is not manifest until the DCs are activated, as for example,by the cytokine interferon-γ and possibly additional signals would comefrom the T cell during antigen presentation (step 3). Thus, although thesame signal is delivered to both “non-suppressor” and “suppressor” DCs,the response of the DC to this signal, either IDO-mediated suppressionof T-cell activation (IDO^(+/POS)), or downregulation of IDO(IDO^(LO/NEG)) such that the DC able to promote T-cell activation,depends on its history in step 2.

This model is consistent with existing models under which DCs undergo a“licensing” or “conditioning” process (corresponding to Step 2), eitherthrough direct cell-cell interaction with a helper T cell (Cella, M., etal., J. Exp. Med., 184: 747-752 (1996); Ridge, J. P., et al., Nature393: 474-478 (1998); Schoenberger, S. P., et al., Nature 393: 480-483(1998); Bennett, S. R., et al, Nature 393: 478-480 (1998)) or viasignals from the local cytokine milieu (Gallucci, S., et al., Nat. Med.5: 1249-1255 (1999); Kourilsky, P, et al., Trends in Immunol., 22:502-509 (2001)). One of the previously undescribed aspects of DCmaturation shown by the model in FIG. 1 is that DCs can be “licensed” tosuppress, and that ability of DCs to become suppressive may be regulatedin vitro by culture conditions. Additionally, the model teaches thatsuppressive and non-suppressive DC populations can be distinguished byIDO expression (and cell surface markers associated with IDO^(+/POS)and/or IDO^(LO/NEG) phenotypes). In vivo, the cytokines drivingcommitment to the suppressor phenotype (e.g., IL10, TGF™) may beprovided by interaction with regulatory T cells (H. Waldmann and S.Cobbold, Immunity 14: 399-406 (2001); Maloy, K. G., et al., NatureImmunol., 2: 816-822 (2001)) or may be present in a generalizedtolerogenic milieu (Kourilsky, P. et al., Trends in Immunol., 22:502-509 (2001); Fiocchi, C., J. Clin. Invest., 108: 523-526 (2001);Chen, W. et al., Immunity 22:14:715-725 (2001); Jonuleit, H. et al.,Trends in Immunol. 22: 394-400 (2001)). In vitro, the regulatorycytokines may be supplied as recombinant cytokines during maturation.

Thus, the present invention teaches that this developmental scheme canbe modeled in vitro to provide IDO⁺ and IDO^(LO) APCs. In humans, DCmaturation has been associated with improved antigen-presenting function(Dhodapkar, M. V., et al., J. Clin. Invest. 105: R9-R14 (2000)) which asoften been assumed to correspond to a loss of tolerogenic activity(Dhodapkar, M. V., et al., J Exper. Med., 193: 233-238 (2001);Roncarolo, M. G. et al., J. Exp. Med. 193: F5-F9 (2001)). However,maturation may not be associated with a loss of tolerogenic activity.Instead, tolerance may be related to an additional signal, as yetundescribed, and which is distinct from other antigen presentation andco-stimulatory factors (Albert, M. L., et al., Nature Immunol., 2: 1010(2001); Shortman, K., et al., Nature Immunol., 2: 988-989 (2001); T.Blankenstein and T. Shuler, Trends Immunol., 23: 171-173 (2002)). Thepresent invention teaches that this additional signal is the expressionof IDO, such that mature DCs that express IDO will be tolerogenic andmature DCs that do not express IDO will be immunogenic.

Thus, the inventors believe that immature DCs are generally tolerogenicbecause in immature DCs, the activating population is ineffective, andtherefore the tolerogenic population, although not optimized, isunopposed. The significant drawbacks to using immature DCs for therapyare that: (1) such cells constitute an uncharacterized mixture of cells,and in many applications even a minor contaminating admixture of theundesired type of APC (i.e. immunogenic instead of tolerogenic) mayrender the APC population unusable or even harmful for the desiredapplication; (2) immature DCs are inherently unstable and may mature(thus, providing an undesired and potentially activating population ofcells); and (3) immature DCs are inherently poor antigen-presentingcells due to their immature status, so the tolerogenic subset does notfunction as effectively as would a pure population of mature tolerogenicDCs.

The present invention therefore provides a method to produce relativelypure populations of suppressive and nonsuppressive APCs. Most DCs andother APC populations contain a mixture of suppressive andnonsuppressive populations. The present invention teaches that theconditions under which the APCs are derived can markedly affect theratio of tolerogenic APCs as compared to immunogenic APCs. Previously,the existence of different tolerogenic and immunogenic subsets in humanscould not be shown, nor was it possible to isolate specific tolerogenic(or immunogenic) subsets of APCs. Thus, the ability to use APCs forclinical applications was severely compromised as the presence ofimmunosuppressive APCs in a preparation of cells being used to enhancethe T cell response (e.g. an anti-tumor vaccine) would result inantagonism of the desired effect. Similarly, the presence of immunogenicAPCs in a preparation of cells being used to suppress the T cellresponse (e.g. transplant therapy) would be counter-productive.

Referring now to FIG. 2, APCs may be treated by culturing underconditions to favor production of (i.e. to select for) APCs that expresshigh levels of IDO (IDO⁺ APCs). In an embodiment, the isolated cells arecultured in medium which is essentially free of serum. Alternatively (oradditionally), the cells may be cultured in the presence of macrophagecolony stimulating factor (MCSF) or granulocyte-macrophage colonystimulating factor (GMCSF). When GMCSF is used, the concentration mayrange from 10 ng/ml to 1000 ng/ml, or more preferably from 50 ng/ml to500 ng/ml. Alternatively (or additionally), the cells may be cultured inthe presence of cytokines such as, but not limited to, TGFβ, IL10, IL 4,IL3, or any combinations thereof.

In an embodiment, the cells are also be treated with an agent to causematuration of those APCs that express high levels of IDO. Preferably,the maturation agents comprise TNFα, IL10, TGFβ, CD40-ligand, activatinganti-CD40 antibodies, cells engineered to express cell surfaceCD40-ligand, proinflammatory bacterial or pathogen products, or anycombination thereof. Thus, these agents may be combined singly, or addedtogether with other agents used for the maturation of DCs (Jonuleit, H.,et al., Eur. J. Immunol., 27: 3135-3142 (1997); Reddy, et al., Blood 90:3640-3646 (1997)).

Following culture and maturation steps, further purification can beaccomplished by differential adherence to a selected substrate chosenand optimized to yield preferential enrichment of the desired IDO⁺population, by methods described herein. Alternatively (oradditionally), the purity of the IDO⁺ population is increased byimmunosorting based on cell-surface antigens that associate with IDO⁺APCs. For example, in an embodiment, CD123 and CCR6 are associated withIDO⁺ APCs and CD14 is associated with IDO^(LO) APCs. Thus, the presentinvention contemplates that IDO⁺ APCs isolated directly from tissues mayonly require maturation and immunosorting to comprise a pure population.Alternatively, when using CD34⁺ APC progenitors, culture may be requiredfor differentiation, and the cytokines chosen for use during culture areselected based on their ability to increase the IDO⁺ population.

FIG. 2 also shows that APCs may be treated by culturing under conditionsto favor production of APCs that express low levels of IDO (IDO^(LO)APCs). For example, cells may be cultured in the presence of GMCSF+IL4and then matured in the presence of TNF-α and CD40 ligand. In anembodiment, APCs are cultured in the presence of neutralizing antibodiesto IL10 and TGFβ. The cells may also be treated with an agent to causematuration of those APCs that express low levels of IDO. Preferably, thematuration agents comprise TNFα, CD40-ligand, activating anti-CD40antibodies, cells engineered to express cell-surface CD40-ligand,proinflammatory bacterial or pathogen products, or any combinationthereof. Thus, these agents may be combined singly, or added togetherwith other agents used for the maturation of DCs (Jonuleit, H., et al.,Eur. J. Immunol., 27: 3135-3142 (1997); Reddy, et al., Blood 90:3640-3646 (1997)).

As described above, and referring now to FIG. 3, the present inventionfurther includes the step of measuring expression of at least one cellsurface antigenic marker that identifies the cells as expressing highlevels of IDO (IDO⁺ APCs) or not expressing high levels of IDO (IDO^(LO)APCs). Preferably, the absence or presence of the cell surface markerassociated with high IDO is used to select for, and isolate, APCs thatexpress high levels of IDO (IDO⁺ APCs) from APCs that do not expresshigh levels of IDO (IDO^(LO) APCs). For example, markers associated withhigh levels of IDO in APCs comprise CD123 and CCR6. A less preferredmarker is CD11c. In an embodiment, the presence of a cell-surface markerassociated with low levels of IDO expression (IDO^(LO)) is used todeplete the preparation of non-tolerogenic cells. Preferably, a markerassociated with low levels of IDO in APCs is CD14. For example, in anembodiment, monocytes may be treated with a cytokine cocktail to inducedifferentiation and expression of IDO. The cells which express highlevels of IDO, and are tolerance-inducing, are then separated from thosecells which do not express IDO using at least one cell surface markerwhich shows a correspondence with IDO expression.

In another embodiment, the expression of uncharacterized cell surfaceproteins is used to facilitate separation of IDO⁺ cells from IDO^(LO)APCs. For example, in an embodiment, cells cultured in serum-free mediumdisplay enhanced adherence of the IDO^(LO) APCs to the plastic culturedish. Thus, by selecting those cells which do not adhere to the plasticdish, a population of IDO⁺ cells is selected.

For example, and referring now to FIG. 4, DCs (immature) cultured inserum-free medium and enriched by non-adherence of IDO⁺ cells to plasticculture wells (i.e. the IDO^(LO) cells adhere) show moderate suppressionof allogeneic T cell proliferation when still immature (FIG. 4A).Suppression may be measured as the finding more APCs (i.e. a low Tcell:APC ratio) results in less T cell proliferation (FIG. 4A).Preferably, the inhibition is substantially due to IDO expression, asevidenced by reversal of the inhibition by 1-methyl-(D)-tryptophan(1-MT), an inhibitor of IDO. In contrast, mature DCs exhibit a muchhigher level of suppression, with suppression occurring even at T cell:APC ratios of 100:1 (FIGS. 4B and 4C). Addition of 1-MT (to inhibit IDOmediated suppression) causes a significant increase in T cellproliferation, to levels greater than immature DCs. Thus, contrary tocurrent models, using the methods of the present invention, maturationactually enhances the suppression of T cells, and the enhancedsuppression is due to IDO.

Referring now to FIG. 5, cultured blood-derived APCs derived in bovineserum based medium (and not fractionated by differential adherence)produce a preparation comprising a mixture of IDO⁺ and IDO^(LO) cells.In an embodiment, a population of immature DCs which express the cellsurface marker CD123 (CD123+) constitutively express immunoreactive IDOprotein (FIGS. 5A and C for myeloid DCs derived in GMCSF+IL4; FIG. 5Bfor macrophages derived in MCSF, respectively). Maturation for 2 dayswith TNFα, or with CD40L, or with a published cocktail of cytokines(Jonuleit H., et al., Eur. J. Immunol., 27: 3135-3142(1997), ormonocyte-condition medium (Reddy et al., Blood 90: 3640-3646 (1997))does not affect IDO expression in the subset of CD123⁺ cells (notshown). In an embodiment, CD123 positive (CD123⁺) cells expressing highlevels of IDO (IDO⁺) also express high levels of the cytokine receptorCCR6 (FIG. 5C). In contrast, cells selected as adhering to the culturedishes comprise primarily IDO^(LO) non-dendritic APCs. Preferably,expression of IDO protein correlates with the ability of the cells tostimulate T cell proliferation as measured by tritiated thymidineincorporation into T cell DNA (FIG. 5E).

Association of Cell Surface Markers with IDO Expression

Because IDO is an intracellular enzyme, expression of the enzyme is noteasy to detect in the intact (i.e. living) cell. Thus, the presentinvention utilizes the discovery that specific cell surface markers areassociated with expression of IDO in antigen-presenting cells (FIG. 3).

For markers associated with cells having high levels of IDO expression(IDO⁺), the marker preferably comprises is a cell surface protein(antigen) for which greater than 75% of the cells express high levels ofIDO by flow cytometry or suppression of T cell proliferation as measuredusing T cell proliferation assays, and more preferably, for whichgreater than 90% of the cells express high levels of IDO by flowcytometry or suppression of T cell proliferation as measured using Tcell proliferation assays, and even more preferably, for which greaterthan 95% of the cells express high levels of IDO by flow cytometry orsuppression of T cell proliferation as measured using T cellproliferation assays.

In an embodiment, the cell surface marker associated with IDO expressionis CD123. CD123 (the IL3-receptor α chain) is expressed on the smallpopulation of lymphoid-lineage “plasmacytoid” dendritic cells inperipheral blood (Liu, Y. J., Cell, 106: 259-262 (2001)), but it is alsoexpressed at lower levels on a poorly-defined subset of myeloid-lineagedendritic cells in vivo (Olweus, J., et al., Proc. Natl. Acad. Sci.,USA, 94: 12551-12556 (1997); Summers, K. L., et al., Am. J. Pathol.,159: 285-295 (2001)).

Referring now to FIG. 5, preferably there is a 1:1 correspondencebetween APCs expressing IDO (IDO⁺) and at least one cell surface marker.For example, in an embodiment, monocyte-derived DCs cultured for 7 daysin GMCSF+IL4 (FIG. 5A) or macrophage-derived DCs cultured in MCSF (FIG.5B) display a discrete subset of cells that express high levels of IDO(IDO⁺), and express the cell surface marker CD123 (FIGS. 5A and B).

In addition, other cell surface markers may be used to identify IDO⁺cells. Thus, in an embodiment, a majority of IDO⁺ APCs express themyeloid-lineage marker CD11c (FIGS. 5A and B).

Preferably, another marker highly associated with IDO expression is thechemokine receptor CCR6. CCR6 is the receptor for the chemokine mip-3α,a chemotactic factor for immature dendritic cells (Yang, D., et al., J.Immunol., 163: 1737-1741 (1999)). Different subsets of dendritic cellsexpress distinct patterns of chemokine receptors (Sozzani, S., et al.,J. Leukocyte Biol. 66: 1-9 (1999)). CCR6 is expressed on CD34⁺-deriveddendritic cells at immature stages of differentiation, and on immaturemonocyte-derived dendritic cells cultured with transforming growthfactor (TGF)-β, but is lost under some conditions when dendritic cellsmature (Yang, D., et al., J. Immunol. 163: 1737-1741 (1999)). Thepresent invention shows that under conditions favoring high expressionof IDO, over 90% of APCs which express IDO also express CCR6 (FIG. 5C).Thus, IDO-expressing, tolerance-inducing APCs may comprise the cellsurface markers CD123, CCR6, and in some cases, CD11c.

The specific pattern of markers that identifies the IDO⁺ (or IDO^(LO))population varies depending on the conditions used to isolate andculture the APCs. For example, CD11c is expressed at low levels inIDO^(LO) cells cultured in bovine calf serum based medium (high seedingdensity and no differential adherence selection; FIG. 5A) but isexpressed at higher levels for the IDO^(LO) culture in serum-free medium(low seeding density and a final fractionation by differential adherenceof non-dendritic APCs to the culture dish).

In an embodiment, enrichment using the cell surface marker alters thecomposition of the preparation such that it displays a higher level ofIDO activity as measured by suppression of a T cell proliferation assay(e.g. an allogenic MLR). For example, and referring now to FIG. 6, CD123enriched (CD123⁺) APCs are markedly less efficient at stimulating T-cellproliferation than either the original unfractionated mixture, or theCD123 depleted subset (CD123^(LO)) that remains after sorting. The lackof T-cell activation is due to IDO expression, as shown by the abilityof the IDO inhibitor, 1-methyl-(D,L)-tryptophan (1-MT), to preventsuppression. Thus, addition of 1-MT allowed the APCs to stimulate T-cellproliferation at near control levels, indicating that IDO is involved inthe suppression. Enrichment may be accomplished by positive selectionusing magnetic beads comprising antibodies to the marker of interest,adhesion, flow cytometric sorting or other selections techniques knownin the art.

Alternatively, when a pure population of IDO⁺ APCs are desired, cellsorting techniques may be used to generate a population of APCs depletedof IDO^(LO) cells using a cell surface antigen that correlates with lowlevels of IDO expression. Preferably, the cell surface antigen is amarker for which greater than 75% of the antigen-bearing cells do notexpress high levels of IDO by flow cytometry or suppression of T cellproliferation assays, more preferably, greater than 90% of theantigen-bearing cells do not express high levels of IDO by flowcytometry or suppression of T cell proliferation assays, and even morepreferably, greater than 95% of the antigen-bearing cells do not expresshigh levels of IDO by flow cytometry or suppression of T cellproliferation assays.

In an embodiment, the marker associated with IDO^(LO) cells comprisesCD14. CD14 (the endotoxin-binding protein receptor) is a well-acceptedmarker for cells of the monocyte-macrophage lineage (Szabolcs, P., etal., Blood 87: 4520-30 (1996)). Monocyte-derived dendritic cellsdown-regulate CD14 to undetectable (background) levels when theydifferentiate along the dendritic cell lineage (Pickl, W. F., et al., J.Immunol. 157: 3850-3859 (1996)). Mature myeloid dendritic cells do notexpress CD14 (K. Shortman and Y.-J. Liu, Nature Reviews: Immunology 2:151-161 (2002)). Thus, in a culture comprising both mature DCs and asecond population of non-dendritic APCs expressing CD14, the expressionof CD14 can be used to distinguish between the two populations.

Thus, in yet an embodiment, a population of cells comprising low levelsof IDO expression (IDO^(LO)) is generated by depleting the APCs of IDO⁺APCs (e.g. by selection with CD123 or other markers associated with highIDO) or by positive selection for markers associated with low IDOexpression, such as CD14.

In yet another embodiment, the expression of uncharacterized cellsurface proteins is used to facilitate separation of IDO⁺ cells fromIDO^(LO) cells. For example, cells cultured in serum-free medium displayenhanced adherence of the IDO^(LO) APCs to the plastic culture dish.Thus, by selecting those cells which do not adhere to the plastic dish,a population of IDO⁺ cells is selected. Examples of substrates which maybe used for selection of cells by adherence include, but is not limitedto, plastic (for example, plastic culture flasks or petri dishes),plastic treated by chemical or other means to facilitate adherence oftissue culture cells (tissue culture plastic), gas-permeable collectionbags used in isolation and storage of blood products, filters, proteincoatings, protein-lipid films and the like.

For example, FIG. 5D shows adherent cells taken from culture ofmonocytes in serum-free medium supplemented with GMCSF+IL4 and maturedwith a cocktail of TNFα, IL1β, IL6 and PGE2 as previously described(Jonuleit, H. et al., Eur. J. Immunol., 27: 3135-3142 (1997)). In thistype of culture, the adherent cells are normally discarded because theyare not dendritic cells (Jonuleit, H., et al., Eur. J. Immunol., 27:3135-3142 (1997); Reddy, A., et al., Blood 90: 3640-3546 (1997)). Thesecells are in fact quite valuable, as they represent a substantiallypurified preparation of IDO^(LO) cells. These cells are not IDO⁺, butthey express markers of APC function (MHC class II, CD80, and CD86) atlevels similar to non-adherent (IDO⁺) cells from the same cultures.Greater than 95% of the IDO^(LO) adherent cells express CD14, whereasless than 10% of the IDO^(LO) adherent cells express CD123 or CCR6.

IDO⁺ APCs as Transplant Therapeutics

Cells which are tolerance-inducing APCs (IDO⁺ APCs), may be used topromote tolerance in a subject. Thus, the invention comprises a methodof preparing cells comprising tolerance-inducing APCs and the use of thecells to enhance immunological tolerance in an individual.

Thus, in one aspect, the present invention comprises a method togenerate APCs for enhancing T cell tolerance towards cells, tissues andspecific antigens in an individual comprising administration of a cellpreparation in which the antigen-presenting cells (APCs) express highlevels of IDO. In this aspect, the present invention relies on thediscovery that APCs expressing high levels of IDO (IDO⁺) are associatedwith reduced ability to activate T-cells (FIG. 6). In this way, IDO⁺APCs are used to increase the likelihood of acceptance of a graft ortransplant from a first donor mammal to a second recipient mammal.

Thus, in one aspect, the present invention comprises a method forenhancing tolerance in a subject comprising the steps of:

(a) isolating antigen-presenting cells (APCs) or their precursors (APCprogenitors) from a first subject;

(b) treating the cells to select for APCs that expressing levels ofindoleamine 2,3-dioxygenase (IDO) enzyme activity sufficient to suppressproliferation of T cells (IDO⁺ APCs); and

(c) administering the treated cells back to the original subject or to asecond subject in an amount effective to generate a tolerance-promotingresponse in the recipient subject.

In an embodiment, a tolerance-promoting response reduces T-cellactivation in the recipient subject. In an embodiment, thetolerance-promoting response prolongs the survival of transplanted cellsor tissues in the recipient subject. In yet another embodiment, thetreated cells are administered back to the original subject, and thetolerance-promoting response reduces the symptoms of an autoimmunedisease in the subject.

As described herein, the present invention also comprises compositionsfor enhancing T cell tolerance. For example, such compositions may beused to promote acceptance of a tissue transplant or graft. Thus, thepresent invention also comprises a composition for enhancing T celltolerance comprising antigen-presenting cells (APCs) selected ascomprising APCs expressing levels of indoleamine 2,3-dioxygenase (IDO)enzyme activity sufficient to suppress proliferation of T cells (IDO+APCs). In one aspect, the compositions are be made by the methods of thepresent invention.

In an embodiment, IDO⁺ APCs of the methods and compositions of thepresent invention are evaluated by measurement of the number of cellsexpressiong IDO. Preferably, the tolerance-inducing IDO⁺ APCs comprise acell population wherein at least 90% APCs expressing IDO at levels atleast 2-fold greater than background, and more preferably at least 95%of the APCs express IDO at levels at least 2-fold greater thanbackground, where background comprises a negative control for IDO.

Alternatively or additionally, IDO activity is quantified using abiological assay. In an embodiment, the tolerance-inducing IDO⁺ APCscomprise suppression of T cell proliferation comprising at least a2-fold increase in T cell proliferation in the presence of an IDOinhibitor as compared to T cell proliferation in the absence of an IDOinhibitor. Preferably, the inhibitors comprise1-methyl-(D,L)-tryptophan, β-(3-benzofuranyl)-(D,L)-alanine,p-[3-benzo(b)thienyl]-(D,L)-alanine, or 6-nitro-(D,L)-tryptophan. Morepreferably, the inhibitors comprises 1-methyl-(D)-tryptophan or6-nitro-(D)-tryptophan.

Preferably, the isolated APCs of the methods and compositions of thepresent invention comprise non-dendritic APCs, mature blood-deriveddendritic cells, mature tissue dendritic cells, monocyte-derivedmacrophages, non-dendritic cells, B cells, plasma cells, or any mixturethereof. Also preferably, the APCs comprise markers of antigenpresentation and co-stimulatory function. Preferably, the APCs areisolated from peripheral blood, bone marrow, lymph nodes or a solidorgan from a mammal. More preferably, the subject is human.

One object of the present invention is to develop tolerance-promotingAPCs that present a specific subset of antigens of interest. Forexample, tolerance-promoting APCs that present antigens from a donor maybe administered to a transplant recipient to promote acceptance of agraft or transplant. Thus, in an embodiment, the subject from which theAPCs or APC progenitors of the methods and compositions of the presentinvention are isolated comprises a tissue donor to a second subject. Inanother embodiment, the APCs or APC progenitors are isolated from asubject with an autoimmune disorder for subsequent preparation of IDO⁺APCs for use in treating the disorder.

Alternatively, the treated APCs of the methods and compositions of thepresent invention are exposed to at least one source of antigen afterisolation from a first subject and selection as IDO⁺ APCs. Preferably,the source of antigen comprises antigens expressed by a donor tissuegraft. Also preferably, the source of antigen comprises protein or othermaterial to which a patient has an autoimmune disorder (see e.g. Yoon,J.-W., et al., Science 284: 1183-1187 (1999) for examples of suchproteins). Thus, in an embodiment, the subject from which the APCs orprogenitor APCs are isolated comprises a patient with an autoimmunedisorder. In an embodiment, the antigen comprises a purified, or asynthetic or recombinant polypeptide representing a specific antigen towhich it is desired that tolerance be induced, or a short syntheticpolypeptide fragment derived from the amino acid sequence of such anantigen. In an embodiment, the isolated APCs are transfected orgenetically engineered to express at least one antigenic polypeptide(see e.g. Nair, S. K., et al., Int. J. Cancer, 82: 121-124 (1999);Heiser, A., et al., J. Clin. Invest., 109: 409-417 (2002)).

In an embodiment, selection of IDO⁺ cells of the methods andcompositions of the present invention is facilitated using a cellsurface marker that identifies the cells as expressing levels of IDOsufficient to suppress T cell proliferation (IDO⁺ APCs) or expressinglevels of IDO not sufficient to suppress T cell proliferation (IDO^(LO)APCs) as described herein. The markers used may include, but are notlimited to, CD123, CCR6, CD11c, CD14, or any combination thereof.Alternatively, the method may include differential adhesion to asubstrate to separate APCs that express low levels of IDO (IDO^(LO)APCs) from APCs that express high levels of IDO (IDO⁺ APCs).

In an embodiment, the composition used to enhance T cell tolerance mayinclude a pharmaceutically acceptable carrier. Alternatively, thecomposition may include one or more immunosuppressive pharmaceuticals ina unit dosage form.

As defined herein, a graft is a tissue specimen for transplantation fromone mammal into another mammal. A host mammal is defined as therecipient of a graft specimen from a donor mammal, wherein the donormammal and the host mammal are distinct entities. The grafts may eitherbe homografts (a graft transplanted between mammals of the same species)or xenografts (a graft transplanted between mammals of the differentspecies).

Isolation of mammalian cells for use as APCs of the present inventionmay be accomplished in accordance with the methods described in theExamples below. In addition, U.S. Pat. Nos. 5,849,589, 6,008,004,6,194,204, and 6,274,378 describe isolation of mixed populations (i.e.not selected as tolerance-inducing) dendritic cells for use with theselection methods described herein and are hereby incorporated byreference in their entirety. Thus, U.S. Pat. No. 5,849,589 describes amethod to induce differentiation of a monocyte into a dendritic cell(DC); U.S. Pat. No. 6,008,004 describes a DC precursor found among bonemarrow CD34⁺ cells; U.S. Pat. No. 6,194,204 describes a serialseparation technique for isolating DC from peripheral blood; and U.S.Pat. No. 6,274,378 describes a method to increase the yield of DCs byculturing in GMCSF and IL-4. Those skilled in the art would be able toimplement modifications to the disclosed methods of isolating cells forpropagation as APCs without the exercise of undo experimentation.

U.S. Pat. Nos. 5,871,728 and 6,224,859, the disclosure of which isincorporated by reference in full herein, describe the isolation ofdendritic cells from a donor for use in a transplant regimen. Incontrast to the present invention, however, the dendritic cells in U.S.Pat. Nos. 5,871,728 and 6,224,859 B1 are cultured under conditions toremain in an immature state and therefore do not present DCs which areoptimized to promote a tolerogenic response, nor are they purified toenrich for the tolerogenic population and/or the immunogenic population.

In an embodiment, autologous tolerogenic APCs are pulsed with anautoantigen (i.e. a protein or other material to which a patient hasdeveloped an autoimmune immunologic response as part of an autoimmunedisorder) and administered back to a patient with an autoimmune disease.In another embodiment, tolerogenic APCs are isolated from the donor of abone marrow transplant or hematopoietic stem-cell transplant andadministered to a second subject who is receiving the transplant so asto prevent graft-versus-host disease in the recipient subject.Alternatively administration of tolerogenic APCs may be used to treatestablished graft-versus-host disease in a transplant recipient. In bothcases, the goal is to initiate the development of a regulatory T cellresponse to a target antigen or set of antigens which will reduce theautoimmune or graft-versus-host T cell responses (H. Waldmann and S.Cobbold, Immunity 14: 399-406 (2001)).

Tolerogenic APCs may be administered prior to transplantation. In anembodiment, prophylactic administration may be commenced as early as 1month prior to transplantation, and more preferably at about 1 weekprior to transplantation. Alternatively, or additionally, administrationmay be at the time of transplantation and for several months followingthe transplantation, and at least several weeks following thetransplantation, or even more preferably, several days followingtransplantation.

Immunosuppressive agents may also be included as part of the transplantregimen. Immunosuppressive reagents are typically administered at thetime of transplantation and at least daily for some period afterwards.The amount of immunosuppressive agent is preferably adjusted based uponthe success of the cell-driven response (i.e. the response as a resultof administration of IDO⁺ APCs.)

Pharmaceutical formulations can be prepared by procedures known in theart. For example, the compounds can be formulated with commonexcipients, diluents (such as phosphate buffered saline), tissue-culturemedium, or carriers (such as autologous plasma or human serum albumin)and administered as a suspension.

The invention contemplates methods of administration which are wellknown in the art. Administration of the APCs of the present inventionmay include, but is not limited to, intravenous, subcutaneous, andintra-tumoral modes of administration. Additionally, the compounds arewell suited to formulation as sustained release dosage forms of at leastpart of the preparation (e.g. immunosuppressive agents). Preferably, thecells are administered in a dose ranging from 5×10⁵ to 5×10¹⁰ cells perdose. More preferably, the cells are administered in a dose ranging from5×10⁶ to 5×10⁹ cells per dose. Even more preferably, the cells areadministered in a dose ranging from 5×10⁷ to 1×10⁸ cells per dose.

IDO^(LO) APCs as Immunogenic Vaccines

The present invention also provides a means to isolate cells enrichedfor immunostimulatory APCs that show enhanced T-cell activation. Forexample, cells depleted of tolerance-inducing APCs can be used asanti-cancer vaccines or anti-viral vaccines to increase the hostresponse to cancer or viral antigens, respectively.

In this aspect, the present invention comprises a method for increasingthe protective immune response to at least one specified antigen in asubject comprising the steps of:

(a) isolating antigen-presenting cells (APCs) or their precursors (APCprogenitors) from a subject;

(b) treating the cells to select for APCs expressing levels ofindoleamine 2,3-dioxygenase (IDO) enzyme activity not sufficient tocause suppression of T cell proliferation (IDO^(LO) APCs); and

(c) administering the treated cells back to the subject in an amounteffective to generate a protective immune response in said subject.

In an embodiment, a protective immune response comprises a reduction insize of a tumor or a reduction in the clinical progression of amalignancy. In another embodiment, a protective immune response isassociated with increased resistance to at least one pathogen. Forexample, such increased resistance to a pathogen may comprise anincreased resistance to infection, a reduced pathogen load, or increasedproduction of pathogen specific antibodies or T cells.

The present invention also comprises compositions for increasing T cellactivation. Such compositions are useful for generating a protectiveimmune response. Thus, in another aspect the present invention comprisesisolated antigen-presenting cells selected as comprising APCs expressinglow levels of indoleamine 2,3-dioxygenase (IDO) enzyme activity(IDO^(LO)), wherein the IDO^(LO) cells comprise a population of APCsexpressing IDO at a level not sufficient to cause suppression of T cellproliferation (IDO^(LO) APCs). The IDO^(LO) APCs may be prepared by themethods described in the present invention or other methods known in theart.

Preferably, IDO^(LO) cells of the methods and compositions of thepresent invention comprise a population of APCs having less than 10% ofthe population expressing IDO at a level of greater than 2-fold overbackground. More preferably, IDO^(LO) cells of the methods andcompositions of the present invention comprise a population of APCshaving less than 5% of the population expressing IDO at a level ofgreater than 2-fold over background. Also preferably, IDO^(LO) APCscomprise non-suppressor activity quantified by a mixed leukocytereaction as less than 1.5 fold increase in T cell proliferation in theabsence of an IDO inhibitor as compared to T cell proliferation in thepresence of an IDO inhibitor. Preferably, the IDO inhibitors comprise1-methyl-(D,L)-tryptophan, β-(3-benzofuranyl)-(D,L)-alanine,β-[3-benzo(b)thienyl]-(D,L)-alanine, or 6-nitro-(DL)-tryptophan. Alsopreferably, the IDO inhibitors comprise 1-methyl-(D)-tryptophan or6-nitro-(D)-tryptophan.

Preferably, the isolated APCs or progenitor APCs comprise matureblood-derived dendritic cells, mature tissue dendritic cells,monocyte-derived macrophages, non-dendritic APCs, B cells, plasma cells,or any mixture thereof. Also preferably, the isolated APCs progenitorAPCs comprise a cell type bearing markers of antigen presentation andcostimulatory function. Also, in preferred embodiments, the APCsprogenitor APCs are isolated from peripheral blood, bone marrow, lymphnodes or a solid organ from a human or other mammal.

In an embodiment the treated APCs of the methods and compositions of thepresent invention are exposed to at least one source of antigen afterisolation from a subject and selection as IDO^(LO) APCs. Preferably, theantigen is a polypeptide expressed by a tumor. Alternatively, theantigen may be expressed by a pathogen. Preferably, the antigencomprises an unpurified tumor or viral preparation. In anotherembodiment, the antigen is a synthetic or recombinant proteinrepresenting a known antigen to which it is desired to induce an immuneresponse, or a short synthetic polypeptide derived from the amino acidsequence of such a protein. In another embodiment, the APCs selected asIDO^(LO) are transfected or genetically engineered to express at leastone such antigenic protein or polypeptide.

In an embodiment, selection of IDO^(LO) cells of the methods andcompositions of the present invention is facilitated using a cellsurface marker that identifies the cells as expressing high levels ofIDO (IDO⁺ APCs) or not expressing high levels of IDO (IDO^(LO) APCs) asdescribed herein. The markers used may include, but are not limited toCD123, CD11c, CCR6, CD14, or any combination thereof. Alternatively, themethod may include differential adhesion to a substrate to separate APCsthat express low levels of IDO (IDO^(LO) APCs) from APCs that expresshigh levels of IDO (IDO⁺ APCs).

As described herein, the APCs selected as IDO^(LO) APCs of the methodsand compositions of the present invention may be exposed to at leastsource of antigen after isolation from said first subject. Preferably,the antigen is a polypeptide expressed by a tumor. Alternatively, theantigen may be expressed by a pathogen. For example, U.S. Pat. Nos.6,228,640, 6,210,662, 6,080,409, 5,994,126, 5,851,756, and 5,582,831describe the manipulation of isolated dendritic cells to produceimmunostimulatory vaccines specific to certain antigens. The disclosuresof U.S. Pat. Nos. 6,228,640, 6,210,662, 6,080,409, 5,994,126, 5,851,756,and 5,582,831 are hereby incorporated in full by reference.

Alternatively, the isolated APCs are transfected or geneticallyengineered to express at least one antigenic polypeptide (see e.g. Nair,S. K., et al., Int. J. Cancer, 82: 121-124 (1999); Heiser, A., et al.,J. Clin. Invest., 109: 409-417 (2002)

Antigens may also be physically introduced into cells. For example, U.S.Pat. No. 6,228,640 B1 describes pulsing DCs with tumor RNA or expressionproducts to prepare APCs comprising expression of specific antigens.Also, U.S. Pat. Nos. 6,210,662 and 6,080,409 describe methods andcompositions generated by activating APCs by contact with a polypeptidecomplex constructed by joining together a dendritic cell-binding protein(GMCSF) and a polypeptide antigen. U.S. Pat. Nos. 5,994,126 and5,851,756 describes a method for producing mature DCs pulsed withantigen, including particulates where the antigenic material isexpressed on the surface of the cells as immunogens for vaccines. U.S.Pat. No. 5,582,831 describes formulation of tumor vaccines by exposingtumor cells to a cross-linking agent to generate antigenic proteincomplexes.

In an embodiment, the isolated APCs of the methods and compositions ofthe present invention further comprise at least one cell surfaceantigenic marker that identifies the cells as expressing low levels ofIDO (IDO^(LO) APCs) or expressing high levels of IDO (IDO⁺ APCs). Themarker may include, but is not limited to CD123, CD11c, CCR6, or anycombination thereof. Alternatively, the method may include differentialadhesion to a substrate to separate APCs that express low levels of IDO(IDO^(LO) APCs) from APCs that express high levels of IDO (IDO+APCs).

The compositions comprising IDO^(LO) APCs may also include apharmaceutically acceptable carrier, where pharmaceutically acceptablecarriers include, but are not limited to the carriers described herein.

Methods and Kits to Measure the Amount of Immunosuppressive Cells in aMixed Population of APCs

The present invention also describes methods to quantitate the levels ofimmunosuppressive APCs in a population of APCs. For most applications itwould be preferable, if not absolutely required, to determine the natureof the cell population being used. For example, when utilizing apreparation of cells for inducing tolerance in a host, a level ofcontaminating IDO^(LO) cells of less than 10%, and more preferably lessthan 5%, is desired. Conversely, when utilizing a preparation of cellsfor increasing the immune response in a host, the level of contaminatingIDO⁺ cells should be determined.

Thus, in one aspect, the present invention comprises a method todetermine the number of tolerance-inducing antigen-presenting cells(APCs) in a cell population comprising measuring the number of cellsexpressing levels of indoleamine 2,3-dioxygenase (IDO) enzyme sufficientto suppress proliferation of T cells (IDO⁺ APCs) in the cell population.In an embodiment, IDO is quantified on a cell-by-cell basis. In anembodiment, IDO is quantified in a bulk population of APCs.

In another aspect, the present invention comprises a kit for determiningthe number of tolerance-inducing antigen-presenting cells (IDO⁺ APCs) ina cell population comprising reagents to measure levels of indoleamine2,3-dioxygenase (IDO) enzyme in the APCs, wherein the reagents arepackaged in at least one individual container.

The immunosuppressive IDO⁺ APCs may also be quantified using abiological assay. Thus, in another aspect, the present inventioncomprises a method to quantify the ability of a population of APCs tosuppress T cell proliferation comprising measuring the ability of thecell population to increase in T cell proliferation in the presence ofan IDO inhibitor as compared to in the absence of an IDO inhibitor. Thepresent invention also comprises a kit for determining the ability of apopulation of APCs to suppress T cell proliferation comprising an IDOinhibitor packaged in at least one individual container. In anembodiment, the kit includes individual assay vessels which provide apre-determined cell density. Preferably, the assay vessels compriseround-bottomed or V-shaped wells.

IDO+APCs and mip-3α as Markers of Tumors

Because tolerance-inducing APCs reduce the host's ability to rejectforeign antigens which are present on tumor cells, the presence oftolerance-inducing APCs in a tumor is associated with a less favorableprognosis than in cases where tolerance-inducing APCs are not present.Thus, the present invention also describes assessing the relative riskof tumor progression by assaying tissue from a tumor or tumor draininglymph node for antigen-presenting cells of myeloid-lineage which havehigh levels of expression of the intracellular enzyme indoleamine2,3-dioxygenase (IDO).

Thus, in another aspect, the present invention comprises a method forassessing the relative risk of tumor progression in a subject comprisingthe steps of:

(a) assaying a sample of tissue from a tumor or tumor draining lymphnode from a subject for expression of the enzyme indoleamine2,3-dioxygenase (IDO); and

(b) correlating the risk of tumor progression to IDO expression in thetissue sample, wherein IDO expression is positively correlated with anincrease in the risk of tumor progression.

In an embodiment, the method further includes identification of cellsurface markers associated with high IDO expression. Preferably, thecell surface markers comprise CD123, CD11c or CCR6.

The present invention also comprises kits for assessing the relativerisk of tumor progression in a subject. For example, in one aspect, thepresent invention comprises a kit for assessing the relative risk oftumor progression in a subject comprising reagents for detection of theenzyme indoleamine 2,3-dioxygenase (IDO) in a sample of tissue from atumor or tumor draining lymph node from a subject, wherein the reagentsare packaged in at least one individual container. Preferably, the kitfurther comprises reagents for detection of cell surface orimmunohistochemical markers associated with high IDO expression by APCs.More preferably, the cell surface markers detected using the kitcomprise CD123, CD11c or CCR6.

The present invention also relies on the discovery that tumor cells thatrecruit tolerance-inducing APCs to the tumor exhibit increasedtolerance. CCR6, a marker highly associated with IDO expression (IDO⁺),is a receptor for the chemokine mip-3α, a chemotactic factor forimmature dendritic cells (D. Yang, O. M. Howard, Q. Chen, J. J.Oppenheim, J. Immunol. 163: 1737-1741 (1999)). Elevated mip-3αexpression has been seen in certain tumors (Bell, D., et al., J. Exp.Med., 190: 1417-1426 (1999)). Thus, tolerance-inducing APCs that expressreceptors for chemoattractant factors secreted by the tumors play a rolein the development of tumor-induced tolerance.

Thus, in another aspect, the present invention also comprises a methodfor assessing the risk of tumor progression in a subject comprising thesteps of:

(a) assaying a sample of tissue from a tumor or tumor draining lymphnodes from a subject for mip-3α expression; and

(b) correlating the risk of tumor progression to mip-3α expression inthe tissue sample, wherein mip-3α expression is positively correlatedwith an increase in the risk of tumor progression.

In another aspect, the present invention comprises a kit for assessingthe relative risk of tumor progression in a subject comprising reagentsfor detection of relative levels of expression of mip-3α in a sample oftissue from a tumor or tumor draining lymph node from a subject, whereinthe reagents are packaged in at least one individual container.

For example, malignant melanoma is a tumor with well-defined T cellantigens but which nevertheless is not eliminated by the immune system.In tumor specimens comprising both primary and metastatic lesions, amajority show infiltration of IDO⁺ cells (FIG. 8B). In addition,recruitment of IDO⁺ dendritic cells is also seen in carcinoma of thebreast, lung, colon and pancreas. Accumulation of these cells occursprimarily around the margins of the tumor and infiltrating along thefibrous stoma, or along the vessels in perivascular cuffs and are not anormal constituent of skin or connective tissue.

Tumor-draining lymph nodes may be a critical site for initiation ofanti-tumor immune responses (Ochsenbein, A. F., et al., Nature 411:1058-1064 (2001)). In an analysis of over 300 tumor-draining lymph nodesfrom 26 patients with malignant melanoma, markedly abnormal accumulationof IDO⁺ cells is seen (FIG. 8C-E). The IDO⁺ cells are found toextensively infiltrate the lymphoid regions of the lymph nodes, largelyconcentrating in the interfollicular and T cell zones. There is alsofrequent accumulation around blood vessels (FIG. 8D) and accumulation atthe interface between lymphoid tissue and tumor metastases or medullarysinuses (FIG. 8E). Normal lymphoid tissue (tonsillectomy specimens withminimal hypertrophy, or lymph node dissections from patients withearly-stage node-negative breast cancer) show only scattered IDO⁺ cells(FIG. 8F), and do not display the extensive focal collections andconfluent areas of IDO⁺ cells seen in tumor-draining nodes. Also, manyprimary and metastatic tumors contain individual tumor cells (FIG. 8I)or entire localized regions within the tumor that express mip-3α byimmunohistochemistry. Quantitative analysis of mip-3α mRNA by real-timePCR confirms mip3α expression in samples of malignant melanoma (M),renal carcinoma (R), and non-small cell lung cancer (L) (FIG. 9).

Thus, the present invention identifies IDO⁺ myeloid dendritic cells as anovel immunoregulatory subset of human APCs. The IDO+dendritic cellpopulation appears to be distinct from the previously described“plasmacytoid” or pre-DC2 dendritic cells (Liu, Y. J., Cell 106, 259-262(2001)). Thus, pre-DC2 express CD123 do not express CD11c, whereas CD11cis found on essentially all IDO⁺ cells in vitro. In addition, while itis possible that that pre-DC2 cells may express IDO in some situations,the majority of IDO-expressing cells appear to be myeloid-derived.

The present invention differs from previous application of tolerogenicDCs in that: (1) mature DCs which are more effective than immature DCsat suppressing T cells are used; (2) a relatively pure preparation oftolerogenic cells (i.e. expressing IDO) is used, rather than apreparation contaminated by non-tolerogenic (IDO^(LO)) cells; and (3)APCs of a type other than DCs may be employed, where the non-dendriticAPCs are selected based on expression of IDO. Thus, in an embodiment,the isolated tolerogenic APCs comprise mature dendritic cells culturedunder conditions optimized to yield a preparation of IDO⁺ cells ormature cells enriched for IDO⁺ cells by selection of IDO⁺ cells from amixed population of IDO⁺/IDO^(LO) cells. Selection of IDO⁺ cells maytake advantage of differential expression of cell surface antigens byeither the IDO⁺ or the IDO^(LO) cells. Thus, cells may be separated byimmunosorting, differential adherence or other methods known in the art

The present invention differs from previous application of immunizing(non-tolerogenic) DCs in that: (a) a relatively pure preparation ofnon-tolerogenic cells (i.e. not expressing immunosuppressive levels ofIDO) is used, rather than a preparation contaminated by tolerogenic(IDO⁺) cells; and (2) APCs of a type other than DCs may be employed,where the non-dendritic APCs are selected based on low or negativeexpression of IDO. Thus, in an embodiment, the isolated non-tolerogenicAPCs comprise mature dendritic cells cultured under conditions optimizedto yield a preparation of IDO^(LO) cells, or mature cells enriched forIDO^(LO) cells by selection of IDO^(LO) cells from a mixed population ofIDO⁺/IDO^(LO) cells. Selection of IDO^(LO) cells may take advantage ofdifferential expression of cell surface antigens by either IDO^(LO) orIDO⁺ cells. Thus, cells may be separated by immunosorting, differentialadherence or other methods known in the art. In another embodiment, theisolated non-tolerogenic APCs comprise mature non-dendritic APCscultured under conditions optimized to yield a preparation of IDO^(LO)cells, with or without further enrichment by selection of IDO^(LO) cellsfrom a mixed population of IDO+/IDO^(LO) cells.

The present invention teaches that IDO-expressing APCs cells aretolerogenic, and are found in large numbers in tumors and draining lymphnodes. One mechanism contributing to the accumulation of these cells maybe tumor-derived mip-3α. Mip-3α is the only known ligand for CCR6, andCCR6 appears to selectively associate with the IDO⁺ dendritic cellphenotype in vitro. The ability to isolate these IDO⁺ and IDO^(LO) APCscells in vitro provides a means to use specific subsets of the IDOexpressing monocytes as therapeutics to either increase or decreaseimmunologic tolerance.

EXAMPLES Example 1 Cell Culture

Human monocytes and lymphocytes were isolated as separate fractions byleukocytapheresis and counterflow elutriation (D. H. Munn et al., J.Exp. Med. 189, 1363-1372 (1999)). Monocytes (typically >95% purity) werecultured in 100 mm tissue culture petri dishes in RPMI-1640 medium with10% newborn calf serum (Hyclone) and including penicillin/streptomycinand glutamine. Cultures received either MCSF (200 U/ml, GeneticsInstitute) on day 0, or GMCSF (50 ng/ml, R&D Systems)+IL4 (50 ng/ml, R&DSystems) on days 0, 2 and 4. For experiments where CCR6 expression wasof interest, cultures received a single dose of GMCSF+IL4 (100 ng/mleach) on day 0, with no further supplementation. Loosely adherentdendritic cells (GMCSF+IL4) were harvested by gentle aspiration;adherent macrophages (MCSF) and non-dendritic APCs (GMCSF+IL4) wereharvested with EDTA. Other cultures were conducted in serum-free medium(X-vivo 15; BioWhitaker, Walkersville, Md.) plus cytokines.

Example 2 Production of Antibodies

All antibodies were obtained commercially except for polyclonalantiserum against human IDO which was manufactured as a work for hire byZCB Inc., Hopkinton, Mass. All commercial antibodies and reagents werefrom BD Biosciences-Pharmingen (San Jose, Calif.) unless specifiedotherwise. For detection of cell surface antigens, DCs weretriple-stained with anti-CD123-biotin (clone 7G3; it was found thatclone 9F5 gave suboptimal results with dendritic cells) followed bystreptavidin-perCP, plus anti-CD11c-allophycocyanin (clone S-HCL-3) oranti-CCR6-fluorescein (clone 53103.111, R&D systems, Minneapolis,Minn.). CCR6 results were also confirmed using a second anti-CCR6antibody (clone 11A9; Pharmingen). For detection of IDO, cells werefixed and permeablized (Cytofix/Cytoperm), and then stained with rabbitanti-IDO antibody prepared against the peptide followed bypolyerythrin-labeled anti-rabbit secondary antibody (JacksonImmunoresearch, West Grove Pa.) cross-adsorbed against mouse, human andbovine IgG, for multiple labeling). Dendritic cells were gated onforward and side scatter to exclude contaminating lymphocytes anddebris.

For preparation of rabbit anti-IDO antibody, the peptideDLIESGQLRERVEKLNMLC (SEQ ID NO: 1) was prepared based on the GenBanksequence of human IDO (M34455) and conjugated to keyhole limpetcyanogen. Rabbits were immunized with conjugated peptide in Freund'sadjuvant (all immunization, antibody preparation and affinitypurification steps were performed as a work for hire (QCB, Inc.,Hopkinton, Mass.). This peptide gave the best results out of severaldifferent sequences screened for their ability to detect human IDO informalin-fixed paraffin-embedded tissue and by flow cytometry.Validation studies showed that this antibody immunoprecipitated theexpected 45 kD band from cell lysates, correlated with IDO mRNA andfunctional enzymatic activity in vitro, identified aninterferon-γ-inducible antigen in two known-positive cell lines (THP-1and HeLa), and detected an antigen by immunohistochemistry which wasspecifically localized to cells with known expression of IDO (thesyncytiotrophoblast cells of human placenta; Y. Kudo and C. A. Boyd,Biochem. Biophys. Acta 1500, 119-124 (2000)). Results were consistentfrom animal to animal, and from lot to lot of antibody.

Example 3 Regulation of IDO Expression During DC Maturation

In humans DCs, maturation has been associated with loss of tolerogenicactivity (Dhodapkar, M. V., et al., J. Exp. Med., 193: 233-238 (2001)).The experiments described in FIG. 4 addressed the issue of whether DCmaturation down-regulates IDO mediated suppressor activity.Monocyte-derived DCs were cultured for 7 days in X-vivo 15 medium withGMCSF+IL4 (non-adherent cell population,>95% IDO⁺, >95% CD123⁺). Duringthe final two days, the cells were either (A) left as immature DCs (noadditions); (B) matured using a cytokine cocktail comprising TNFα, IL1β,IL6 and PGE2 (Jonuleit, H. et al., Eur. J. Immunol., 27: 3135-3142(1997)); or (C) matured using monocyte-conditioned medium (Reddy, A., etal., Blood 90: 3640-3546 (1997)). Each group was harvested and added to5×10⁵ allogeneic T cells in V-bottom 96 well microtiter wells in 200 μlmedium (10% fetal calf serum in RPMI)). Differing numbers of DCs wereadded to a fixed number of T cells to produce the T cell to APC ratiosshown (thus, the greater number of APCs are on the left of the axis, thelesser numbers on the right). Replicate groups of wells received either200 μM 1-methyl-(D)-tyrptophan (1-MT) (□), or saline control (Δ), todisclose IDO-mediated suppression (defined as the amount ofproliferation restored at each T cell: APC ratio by adding 1-MT andshown for one point as an arrow in panel B). After 5 days, T cellproliferation was measured as the incorporation of tritiated thymidine(Munn, D. H. et al., J. Exp. Med., 189: 1363-1372 (1999).

FIG. 4A shows that higher numbers of immature dendritic cells (lowerAPC: T cell ratios) were associated with increased IDO mediatedsuppression (shown as the reduced T cell proliferation at the lower Tcell:APC cell ratios, and as enhancement of proliferation when1-methyl-(D)-tryptophan was added). In FIGS. 4B and 4C, the DCs werematured. It can be seen that the mature DCs show greater IDO mediatedsuppression (with suppression occurring at T cell:APC cell ratios as lowas 100:1). Although the mature DCs were highly suppressive due to thepresence of IDO, the mature forms actually function better asantigen-presenting cells compared to the immature form, as revealed bythe higher T cell proliferation achieved when suppression was preventedby 1-MT (i.e. the difference between □ and Δ for each experiment). Thus,mature DCs derived under conditions optimized in accordance with theinvention were both more suppressive and more effective as APCs thanimmature DCs. Both of these attributes are desirable for induction oftolerance.

Example 4 Co-Expression of IDO with Cell Surface Markers CD123, CC11cand CCR61n Myeloid APCs

Expression of IDO in immature monocyte-derived (myeloid) dendritic cells(Dhodapkar, M. V., et al., J. Exp. Med. 193: 233-238 (2001)) and inimmunosuppressive monocyte-derived macrophages (Munn, D. H., et al., J.Exp. Med. 189: 1363-1372 (1999)) was analyzed. FIG. 5 shows theexpression of IDO and CCR6 by myeloid antigen-presenting cells whichexpress the cell surface antigen CD123 (CD123⁺). Human monocytes werecultured as described above (Example 1) for 7 days with GMCSF^(+IL)4 toproduce myeloid dendritic cells (FIGS. 5A and 5C), or for 7 days in MCSFto produce macrophages (FIG. 5B) (Munn, D. H., et al., J. Exp. Med. 189:1363-1372 (1999)). Prior to analysis, cells were treated withinterferon-γ (INFγ) for 18 hrs to induce maximal expression of IDO.Harvested cells were triple-stained for CD123, CD11c and IDO. For FIG.5D, cells were cultured as in Example 1 except in a commercial,FDA-approved serum-free medium formulation (X-vivo 15; BioWhitaker,Waldersville, Md.).

As shown in FIGS. 5A and B, both preparations contained a discretesubset of cells that expressed IDO following interferon-γ treatment.Characterization of these IDO⁺ cells showed that they all expressed themyeloid-lineage marker CD11c, and CD123, wherein >90% of the IDO⁺expressed the myeloid-lineage marker CD11c and >99% of the IDO⁺ cellsexpressed CD123. To test whether these were truly DCs, additionalphenotyping was performed. Cells were matured with TNFα during the last2 days of culture, in order to upregulate maturation and costimulatorymarkers, and non-adherent cells were harvested. Following TNFα, allnon-adherent cells displayed a veiled/dendritic morphology. Three-colorphenotyping showed that the CD123⁺/IDO⁺ subset of cells were uniformlyCD14⁻ and CD83⁺, consistent with their identity as dendritic cells;uniformly CD11b⁺ and BDCA-2⁻ (Dzionek, A., et al., J. Immunol, 165:6037-6046 (2000)) consistent with their myeloid origin, anddistinguishing them from plasmacytoid DCs (Grouard, G., et al., J. Exp.Med., 185: 1101-1111 (1997)); and 100% positive for CD80, CD86 and MHCclass II (HLA-DR). Under these conditions (bovine serum-based medium)CD11c expression was high on the CD123⁺ subset, and was lower andvariable on the CD123^(LO) subset.

In addition, when monocytes were cultured under conditions that favoredexpression of CCR6 (serum-free medium, single-dose GMCSF+IL4), theCD123⁺/IDO⁺ cells were almost all (>99%) CCR6⁺ (FIG. 5C). Forexperiments where CCR6 expression was of interest, cultures received asingle dose of GMCSF+IL4 (100 ng/ml each) on day 0, with no furthersupplementation. Moreover, within the myeloid dendritic cell population,IDO and CCR6 expression were coincident. T and B cells, which alsoexpress CCR6, were excluded from analysis by forward and side scatterproperties during flow cytometric analysis. The cell-surface CCR6 onthese cells was functional: when immature dendritic cells containing amixture of CCR6-positive and -negative cells were placed in chemotaxischambers, the CCR6-positive cells selectively migrated in response to amip3α gradient (data not shown).

Expression of IDO is not found in all types of dendritic cells. Analysisof plasmacytoid dendritic cells, defined as the population of peripheralblood mononuclear cells expressing CD123 but negative forlineage-specific markers (Lin-1 marker cocktail, BD-Pharmingen),revealed no detectable expression of IDO following activation for 6 hrsor 24 hrs with interferon-γ, in the presence of IL3 to support viability(data not shown). Moreover, when the adherent cells (comprising thenon-dendritic APC population) from cultures of peripheral bloodmononuclear cells in GMCSF+IL4 were examined, they were found to expressvery low levels of IDO and little CD 123 (FIG. 5D). Additionalphenotyping of the non-dendritic APCs showed that they were uniformlyCD14-positive and CD83-negative (thus, distinguishing them unambiguouslyfrom mature dendritic cells, but were >95% positive for CD80 and CD86(thus, identifying them as mature antigen-presenting cells), andexpressed high levels of the MHC class II antigen HLA-DR (furtherdistinguishing them from immature dendritic cells, and identifying themas mature APCs). Consistent with the observed absence of IDO expression,these non-dendritic APCs showed excellent APC function without anydetectable IDO-mediated suppression (i.e. no increase in proliferationin the presence of 1-methyl-(D)-typtophan (1-MT) (FIG. 5E), wherestippled bars are standard MLR and striped bars are the MLR with 1-MT.The T cell: APC ratio in FIG. 5E was the same (20:1) for both DCs andnon-dendritic APCs and both populations were isolated from the sameculture of mononuclear cells in GMCSF+IL4 and tested against the samepopulation of T cells in parallel MLRs.

Example 5 Suppression of Allogeneic T Cell Proliferation by DendriticCells Expressing IDO

The experiments shown in the previous example demonstrated that distinctIDO⁺ and IDO^(LO) subsets can exist in the same preparation of dendriticcells. This example shows that IDO expressing dendritic cells from sucha mixture suppress allogeneic T cell proliferation (FIG. 6).

Myeloid dendritic cells (derived in bovine serum-based medium as in FIG.5A) were activated for 24 hrs with TNFα (10 ng/ml, BD), labeled withanti-CD123 antibody, then enriched by sorting with goat anti-mousesecondary antibody conjugated to magnetic beads (Miltenyi Biotec). Sinceexpression of cell-surface CD123 correlated closely with possession ofinducible IDO, immunomagnetic sorting based on CD123 was used to enrichfor the IDO⁺ subset. Cells selected as CD123⁺ cells (85-90% purity) byimmunomagnetic sorting were then tested as stimulators in an allogeneicMLR. Dot-plots show analysis before (“Pre-sort”) and after (“CD123⁺”)enrichment (FIG. 6A).

The CD123⁺-enriched cells were used as APCs in an allogeneic MLR.Dendritic cells were mixed with purified allogeneic lymphocytes (<1%monocytes, 80-85% T cells, with the balance being B and natural killer(NK) cells) at a 1:10 ratio in V-bottom culture wells. After 5 days,proliferation was measured by 4 hr thymidine incorporation assay.Controls shown include the unfractionated population (“Pre-sort”) andthe cells remaining after positive selection for CD123 (“Depleted”).Typically <10% of the “Depleted” cell population was CD123⁺. Solid barsshow conventional MLR; open bars show MLR in the presence of 200 uM1-methyl-(D,L)-tryptophan (1-MT) (Sigma-Aldrich, St. Louis, Mo.), aninhibitor of IDO. In a similar set of experiments, 3 different pairs ofdonors, each allogeneic to the other, and each pair pre-tested toproduce an active MLR were used without 1-MT (solid bars) or with 1-MT(open bars) (FIG. 6C).

As shown in FIGS. 6B and C, the CD123-enriched (CD123⁺) IDO⁺ cells weremarkedly less efficient at stimulating T cell proliferation than eitherthe original unfractionated mixture, or than the CD123-depleted IDO^(LO)subset that remained after sorting. To test the hypothesis that thislack of proliferation was due to active suppression by IDO, cultureswere treated with 1-methyl-(D,L)-tryptophan (1-MT), a pharmacologicinhibitor of IDO. In the presence of 1-methyl-(D,L)-tryptophan, theCD123⁺ dendritic cells stimulated proliferation at or near controllevels (FIGS. 6B and C), demonstrating that IDO causes suppression.

Example 6 Sorting on the Basis of Cell Surface CD123⁺ Results inEnrichment of the IDO⁺ Population

This example shows that sorting dendritic cells to select for CD123⁺cells results in a population of cells which exhibits high levels of IDOexpression. In this experiment, monocyte derived dendritic cells (DCs)were labeled with anti-CD123 antibody and selected using immunomagneticsorting. Immediately after sorting, cells were dual-stained for CD123(surface) and IDO (intracellular). As seen in FIG. 7, the positivelyselected cells were approximately 90% CD123⁺. In addition, all (>99%) ofthe cells showed high levels of IDO as detected by staining. Incontrast, the residual cells following CD123 depletion were mostly CD123negative, and expressed low, or undetectable levels of IDO. Thus, it wasfound that the CD123 depleted population had 10-100 fold lower levels ofIDO than the CD123⁺ population (FIG. 7).

Example 7 Detection of IDO-Expressing CD123⁺ Dendritic Cells in HumanTumors and Draining Lymph Nodes

This example shows that CD123⁺ dendritic are associated with humantumors and draining lymph nodes. Samples of tumor and tumor-draininglymph nodes were chosen from patients with malignant melanoma, a tumorwith well-defined T cell antigens but which nevertheless is noteliminated by the immune system. Recruitment of IDO⁺ dendritic cells wasalso seen in carcinoma of the breast, lung, colon and pancreas, tumorswhich account for almost half of all cancer deaths in the United States.

Archival pathology specimens were stained for expression of IDO andother antigens by immunohistochemistry. Paraffin sections (5 um) weredeparaffinized, treated for 8 min with proteinase K (Dako, Carpinteria,Calif.), and stained with rabbit anti-human IDO antibody (5 μg/ml inTris buffered saline with 0.05% Tween-20 and 10% goat serum). Detectionwas via secondary antibody conjugated to alkaline phosphatase(LSAB-rabbit kit, Dako) with Fast Red chromogen, or horseradishperoxidase (LSAB2, Dako) and diaminobenzidine. Negative controlsconsisted of the anti-IDO antibody neutralized with a 100-fold molarexcess of the immunizing peptide. Mip-3α (goat polyclonal, R&D Systems)was used following antigen retrieval with citrate (Target, Dako). Fordual-staining, the first antibody was applied following appropriateantigen retrieval and detected with peroxidase/diaminobenzidine. Stainedslides were then subjected to additional antigen retrieval if requiredand stained for the second antigen by alkaline phosphatase/Fast Red.Secondary antibodies were cross-adsorbed against mouse, human and bovineIgG for multiple labeling.

In all of these studies, the IDO⁺ cells observed appeared to be of thesame cell type, displaying a characteristic morphology resemblingplasmacytoid DCs (Cella, M., et al., Nature Medicine 5: 919-923 (1999));Grouard, G., et al., J. Exp. Med., 185: 1101-1111 (1997); Facchetti, F.,et al., J. Pathol., 158: 57-65 (1989)). They were neither histiocytic(macrophage-like) nor classically dendritic in appearance, and did notmark with Ham56 (a macrophage marker) or S100 (a marker of classicaldendritic cells) (data not shown). Shown in FIG. 8A is a known positivecontrol for detection of IDO (brown, diaminobenzidine chromogen) insyncytiotrophoblast cells of term human placenta (Kudo, Y., et al.,Biochem. Biophys. Acta 1500: 119-124 (2000)). The inset shows the sametissue, but with anti-IDO antibody neutralized by an excess of theimmunizing peptide. (Bar=100 um, inset at half-scale).

For normal lymphoid tissue controls, non-inflamed tonsil (from routinetonsillectomy, pathologic diagnosis of “hypertrophy”) and lymph nodesfrom patients with node-negative breast cancer who never developedmetastases or recurred in 5 years following resection were used.Although not technically “normal,” these specimens were the leastinflamed lymphoid tissue removed in routine clinical practice. Over 20of these specimens have been examined, and they consistently show onlyrare, scattered IDO⁺ cells, usually localized to germinal centers (FIG.8F).

For tumor-draining lymph nodes from regional lymph node dissections inpatients with a variety of solid tumors (breast, colon, lung, andpancreatic carcinoma, and malignant melanoma) were used. Most of thesenodes were not mapped by lymphoscintigraphy, so not all would actuallydrain the tumor, but many would. In all 5 types of tumor examined,approximately one-third to one-half of patients had one or more lymphnodes showing markedly abnormal collections of IDO⁺ cells (FIG. 8C). Inthese nodes, often massive infiltrates of IDO⁺ cells were localized tothe perifollicular and interfollicular areas, often adjacent to themedullary sinuses, or collected in dense perivascular cuffs around highendothelial venules (FIG. 8D). In 328 lymph nodes from 26 patients withmelanoma, abnormal infiltration of IDO⁺ cells was found in 14/26patients. Where micro-metastases to lymph nodes were present, IDO⁺ cellsoften surrounded the margins of the tumor collections (FIG. 8E).

Thus, FIG. 8C shows a draining lymph node of a malignant melanomashowing accumulation of IDO-expressing cells (red) in the lymphoid andperivascular regions of the node, but sparing the macrophage-richsinuses (asterisk). (Bar=100 um). FIG. 8D shows a higher magnificationof panel C, showing a characteristic collection of IDO-expressing cellsaround a high-endothelial venule (V). (Bar=50 um). FIG. 8E shows alow-power view of a draining lymph node containing heavily pigmentedmetastatic melanoma cells (endogenous melanin, black; darkest signal),with confluent infiltration of IDO-expressing cells (red; next darkestsignal) around the tumor deposits.

For solid tumors, 14 malignant melanoma tumors were examined with 8/14found to display collections of IDO⁺ cells at the site of the primarytumor. Usually these were in the connective tissue immediatelysurrounding the tumor (FIG. 8B, arrows) rather than in the tumorparenchyma itself. Similar infiltrates of IDO⁺ cells have been seen inbreast, lung, and pancreatic tumors.

For inflamed lymphoid tissue tonsils known to be infected (either byclinical diagnosis or by histopathologic diagnosis) and lymph nodebiopsies bearing the histopathologic diagnosis of “reactive lymph node”were examined. Many of these specimens showed focal or regionalcollections of IDO⁺ cells. In tonsils these collections frequentlyoccurred in a subepithelial location beneath the mucosa and along thecrypts (not shown).

Finally, gut-associated lymphoid tissue from the (human) small intestinewas examined since IDO⁺ DCs derived in vitro expressed CCR6, and micewith a targeted disruption of CCR6 (Varona, R., et al., J. Clin.Invest., 107: R37-45 (2001)) fail to recruit a population of myeloid DCsinto the lymphoid tissue of the gut. FIG. 6G shows prominent collectionsof IDO⁺ cells in the lamina propria overlying lymphoid aggregates in thegut, congregating near cells expressing mip-3α (the ligand for CCR6(Sozzani, S. et al., J Leukocyte Biol. 66: 1-9 (1999); Zlotnik, A., etal., Immunity 12: 121-127 (2000)).

Thus, it was found that cells expressing IDO (and CCR6) co-localizedwith cells expressing mip-3α. Sections of normal human small intestinewere used as a positive control for mip-3α expression, since murinestudies have shown that mip-3α is highly expressed in the subepithelialtissues overlying mucosal lymphoid aggregates of the small intestine (A.Iwasaki and B. L. Kelsall, J. Exp. Med. 191: 1381-1394 (2000)). As shownin FIG. 8G, the corresponding region in humans contained focalcollections of cells expressing mip-3α, along with extensiveco-localization of IDO-expressing dendritic cells to the same areas.Thus, FIGS. 8G and H shows co-localization of cells expressing IDO(brown; darkest cytoplasmic signal) and mip-3α (red; next darkestsignal) in the lamina propria of the small intestine, particularly inthe subepithelial areas overlying mucosal lymphoid aggregates (LA). FIG.8H shows a higher magnification of the region in panel G indicated bythe arrow. Bar=50 μm.

Examination of mip-3α expression in malignancies showed that manyprimary and metastatic tumors contained individual tumor cells (FIG. 81)or entire localized regions within the tumor that expressed mip-3α byimmunohistochemistry. Although both mip-3α and IDO expressing cells arefound in the tumor, they did not appear to be located in identicalcells. Thus, FIG. 8I shows expression of mip-3α: (red) (arrow, lowerright) by tumor cells in a lesion of malignant melanoma metastatic tolymph node. The mip-3α⁺ cells are scattered throughout the tumor (T),while the IDO⁺ cells are congregated at the margins of the metastasisbut confined to the residual lymph node tissue (LN). FIG. 8J shows ahigher magnification of the region in panel M indicated by the arrow,showing mip-3α expression in tumor cells where the bar=50 m.

In addition, the morphology of these cells showed that they were tumorcells, not stroma or other host-derived cells. Quantitative analysis ofmip-3α mRNA by real-time PCR confirmed expression in 8/18 samples ofmalignant melanoma (see Example 8). To ensure that this was not anidiosyncratic property of melanomas, additional RNA samples wereanalyzed from tumors of unrelated histology and cell of origin (renalcell carcinoma and non-small cell lung cancer). This confirmed that avariety of tumor types express mip-3α (D. Bell et al., J. Exp. Med. 190,1417-1426 (1999)).

Example 8 Quantification of mip-3α Expression in Human Tumors

It was found that human tumors express mip-3α. RNA was isolated frommelanomas (M, n=18), renal cell carcinomas (R, n=19) or non-small celllung cancers (L, n=9) and analyzed for expression of mip-3α byquantitative RT-PCR (FIG. 9). The RNA was reverse-transcribed usingrandom hexamer priming and analyzed using the LightCycler real-time PCRsystem (Roche, Indianapolis, Ind.) and FastStart DNA Amplification Kit(SYBR Green 1, Roche). The primers used were: GAPDH (GenBank GI:7669491,sense basepairs (bp) 87-104, antisense bp 289-307) and mip-3α (GenBankGI:4759075, sense bp 103-121, antisense bp410-428). Standard curves wereprepared from U937 cells induced with phorbol myristate acetate for 24hrs, and were linear (r=−0.99) in the range of 100 pg to 100 ng totalRNA.

It was found that there was an increase in mip-3α mRNA in all threetumor types assayed (FIG. 9). To permit comparison between differentsamples the data are presented as an index, calculated as the ratio ofmip-3α to the GAPDH housekeeping gene in each sample, normalized to thevalue of the control cell line (resting U937 cells). The data shown thusrepresent fold increase of mip-3α expression over that for GAPDH.

The invention has been described in detail with particular reference topreferred embodiments thereof, but it will be understood that variationsand modifications can be effected within the spirit and scope of theinvention. References cited herein are incorporated in their entirety byreference unless otherwise noted.

1. A method for assessing the relative risk of tumor progression in asubject comprising the steps of: (a) assaying a sample of tissue from atumor or tumor draining lymph node from a subject for cells that expressthe enzyme indoleamine 2,3-dioxygenase (IDO); and (b) correlating therisk of tumor progression to IDO expression in the tissue sample,wherein IDO expression is positively correlated with an increase in therisk of tumor progression.
 2. The method of claim 1, wherein step (a)comprises quantification of cells expressing cell-surface orimmunhistochemical markers associated with expression of IDO in antigenpresenting cells (APCs).
 3. The method of claim 2, wherein the cellsurface markers comprise at least one of the following combinations: (a)CD11c and CD123; or (b) CD11c and CCR6.
 4. The method of claim 1,wherein IDO expression is quantified using an anti-IDO antibody.
 5. Themethod of claim 4, wherein the anti-IDO antibody is directly labeledwith at least one of a chemical, fluorescent, or an enzymatic moiety. 6.The method of claim 4, wherein the anti-IDO antibody is detected with alabeled secondary antibody that recognizes the anti-IDO antibody.
 7. Themethod of claim 4, wherein IDO expression is quantified using anELISA-based assay of cell extracts isolated from the sample.
 8. Themethod of claim 1, wherein IDO expression is quantified by in-situhybridization with an oligonucleotide probe that hybridizes to IDO mRNA.9. The method of claim 1, wherein IDO expression is quantified byreverse-transcriptase PCR with oligonucleotide primers that hybridize toIDO cDNA.
 10. The method of claim 1, wherein IDO expression isquantified by measuring IDO enzymatic activity.
 11. A method todetermine the number of antigen presenting cells that express elevatedlevels of indoleamine 2,3-dioxygenase (IDO+ APCs) in a human sample oftumor or tumor draining lymph node comprising detecting cells thatexpress at least one of: (a) IDO; (b) both cell surface markers CD11cand CD123; or (c) both cell surface markers CD11c and CCR6.
 12. Themethod of claim 11, wherein quantification of the IDO⁺ APCs is performedusing an antibody or antibodies that recognize the at least one of: (a)IDO; (b) both cell surface markers CD11c and CD123; or (c) both cellsurface markers CD11c and CCR6.
 13. The method of claim 12, wherein theantibody or antibodies are directly labeled with a chemical,fluorescent, or an enzymatic moiety.
 14. The method of claim 12, whereinthe antibody or antibodies are detected with a labeled secondaryantibody, wherein the secondary antibody recognizes the antibody orantibodies that recognize the at least one of: (a) IDO; (b) both cellsurface markers CD11c and CD123; or (c) both cell surface markers CD11cand CCR6.
 15. The method of claim 11, wherein IDO in the sample isquantified using an ELISA-based assay of cell extracts isolated from thesample.
 16. The method of claim 11, wherein IDO in the sample isquantified by in-situ hybridization with a probe specific to IDO mRNA.17. The method of claim 11, wherein IDO in the sample is quantified byreverse-transcriptase PCR using primers specific to IDO cDNA.
 18. Themethod of claim 11, wherein IDO in the sample is quantified by measuringIDO enzymatic activity.
 19. A method for assessing the relative risk oftumor progression in a subject comprising quantifying the number ofcells in a tumor or a tumor-draining lymph node expressing at least oneof the following combinations of markers: (a) IDO; (b) CD11c and CD123:or (c) CD11c and CCR6.
 20. The method of claim 19, wherein the markersare detected by flow cytometry or immunohistochemistry.